diff --git a/frontend/public/locales/en-GB/translation.json b/frontend/public/locales/en-GB/translation.json
index f6f8d828c..4fdc5b79b 100644
--- a/frontend/public/locales/en-GB/translation.json
+++ b/frontend/public/locales/en-GB/translation.json
@@ -1992,6 +1992,7 @@
       "2": "Document 2"
     },
     "submit": "Compare",
+    "newLine": "new-line",
     "complex": {
       "message": "One or both of the provided documents are large files, accuracy of comparison may be reduced"
     },
diff --git a/frontend/public/locales/en-US/translation.json b/frontend/public/locales/en-US/translation.json
index b57f6cf59..535b0fce4 100644
--- a/frontend/public/locales/en-US/translation.json
+++ b/frontend/public/locales/en-US/translation.json
@@ -1321,6 +1321,7 @@
       "removed": "Removed from base",
       "added": "Added in comparison"
     },
+    "newLine": "new-line",
     "summary": {
       "baseHeading": "Base document",
       "comparisonHeading": "Comparison document",
diff --git a/frontend/src/components/tools/compare/CompareDocumentPane.tsx b/frontend/src/components/tools/compare/CompareDocumentPane.tsx
index 1dc9756ac..81253b247 100644
--- a/frontend/src/components/tools/compare/CompareDocumentPane.tsx
+++ b/frontend/src/components/tools/compare/CompareDocumentPane.tsx
@@ -229,7 +229,7 @@ const CompareDocumentPane = ({
                     style={{ width: `${Math.round(page.width * fit)}px` }}
                   >
                     <div
-                      className="compare-diff-page__inner"
+                      className={`compare-diff-page__inner compare-diff-page__inner--${pane}`}
                       style={{ transform: `translate(${-panX}px, ${-panY}px) scale(${zoom})`, transformOrigin: 'top left' }}
                     >
                       <img
diff --git a/frontend/src/components/tools/compare/CompareNavigationDropdown.tsx b/frontend/src/components/tools/compare/CompareNavigationDropdown.tsx
index ca514d73e..9265617ea 100644
--- a/frontend/src/components/tools/compare/CompareNavigationDropdown.tsx
+++ b/frontend/src/components/tools/compare/CompareNavigationDropdown.tsx
@@ -1,5 +1,6 @@
 import { Combobox, ScrollArea, useCombobox } from '@mantine/core';
 import { useMemo, useState } from 'react';
+import { useTranslation } from 'react-i18next';
 
 interface NavigationDropdownProps {
   changes: Array<{ value: string; label: string; pageNumber?: number }>;
@@ -14,6 +15,8 @@ const CompareNavigationDropdown = ({
   className,
   onNavigate,
 }: NavigationDropdownProps) => {
+  const { t } = useTranslation();
+  const newLineLabel = t('compare.newLine', 'new-line');
   const combobox = useCombobox({
     onDropdownClose: () => combobox.resetSelectedOption(),
   });
@@ -50,13 +53,21 @@ const CompareNavigationDropdown = ({
   const [query, setQuery] = useState('');
 
   const normalizedChanges = useMemo(() => {
+    // Helper to strip localized new-line marker occurrences from labels
+    const esc = (s: string) => s.replace(/[.*+?^${}()|[\]\\]/g, '\\$&');
+    const stripNewLine = (s: string) =>
+      s
+        .replace(new RegExp(`\\b${esc(newLineLabel)}\\b`, 'gi'), ' ')
+        .replace(/\s+/g, ' ')
+        .trim();
+
     const cleaned = changes
-      .map((c) => ({ value: c.value, label: sanitize(c.label), pageNumber: c.pageNumber }))
-      .filter((c) => isMeaningful(c.label));
+      .map((c) => ({ value: c.value, label: stripNewLine(sanitize(c.label)), pageNumber: c.pageNumber }))
+      .filter((c) => isMeaningful(c.label) && c.label.length > 0 && c.label.toLowerCase() !== newLineLabel.toLowerCase());
     const q = sanitize(query).toLowerCase();
     if (!q) return cleaned;
     return cleaned.filter((c) => c.label.toLowerCase().includes(q));
-  }, [changes, query]);
+  }, [changes, query, newLineLabel]);
 
   return (
     <Combobox
diff --git a/frontend/src/components/tools/compare/hooks/useCompareChangeNavigation.ts b/frontend/src/components/tools/compare/hooks/useCompareChangeNavigation.ts
index 56494a23b..b4096cd6b 100644
--- a/frontend/src/components/tools/compare/hooks/useCompareChangeNavigation.ts
+++ b/frontend/src/components/tools/compare/hooks/useCompareChangeNavigation.ts
@@ -72,6 +72,39 @@ export const useCompareChangeNavigation = (
 
         container.scrollTo({ top: desiredTop, left: desiredLeft, behavior: 'smooth' });
 
+        // Also scroll the peer container to the corresponding location in the
+        // other PDF (same page and approximate vertical position within page),
+        // not just the same list/scroll position.
+        const peerRef = pane === 'base' ? comparisonScrollRef : baseScrollRef;
+        const peer = peerRef.current;
+        if (peer) {
+          // Use the first node as the anchor
+          const anchor = nodes[0];
+          const pageEl = anchor.closest('.compare-diff-page') as HTMLElement | null;
+          const pageNumAttr = pageEl?.getAttribute('data-page-number');
+          const topPercent = parseFloat((anchor as HTMLElement).style.top || '0');
+          if (pageNumAttr) {
+            const peerPageEl = peer.querySelector(
+              `.compare-diff-page[data-page-number="${pageNumAttr}"]`
+            ) as HTMLElement | null;
+            const peerInner = peerPageEl?.querySelector('.compare-diff-page__inner') as HTMLElement | null;
+            if (peerPageEl && peerInner) {
+              const innerRect = peerInner.getBoundingClientRect();
+              const innerHeight = Math.max(1, innerRect.height);
+              const absoluteTopInPage = (topPercent / 100) * innerHeight;
+              const peerDesiredTop = Math.max(
+                0,
+                peerPageEl.offsetTop + absoluteTopInPage - peer.clientHeight / 2
+              );
+              peer.scrollTo({ top: peerDesiredTop, behavior: 'smooth' });
+            } else if (peerPageEl) {
+              // Fallback: Scroll to page top
+              const top = Math.max(0, peerPageEl.offsetTop - Math.round(peer.clientHeight * 0.2));
+              peer.scrollTo({ top, behavior: 'smooth' });
+            }
+          }
+        }
+
         const groupsByInner = new Map<HTMLElement, HTMLElement[]>();
         nodes.forEach((element) => {
           const inner = element.closest('.compare-diff-page__inner') as HTMLElement | null;
diff --git a/frontend/src/components/tools/compare/hooks/useCompareHighlights.ts b/frontend/src/components/tools/compare/hooks/useCompareHighlights.ts
index f86f5d885..c0bf49f08 100644
--- a/frontend/src/components/tools/compare/hooks/useCompareHighlights.ts
+++ b/frontend/src/components/tools/compare/hooks/useCompareHighlights.ts
@@ -7,6 +7,7 @@ import type {
 import type { CompareChangeOption } from '../../../../types/compareWorkbench';
 import type { PagePreview } from '../../../../hooks/useProgressivePagePreviews';
 import type { WordHighlightEntry } from '../types';
+import { PARAGRAPH_SENTINEL } from '../../../../types/compare';
 
 interface TokenGroupMap {
   base: Map<number, string>;
@@ -42,22 +43,32 @@ const buildWordChanges = (
   for (let i = 0; i < tokens.length; i += 1) {
     const token = tokens[i];
     if (token.type === targetType) {
-      const startIndex = metadataIndex;
       const parts: string[] = [];
       const runIndices: number[] = [];
       const pageNumber = metadata[metadataIndex]?.page ?? 1;
       while (i < tokens.length && tokens[i].type === targetType) {
-        parts.push(tokens[i].text);
-        runIndices.push(metadataIndex);
+        const t = tokens[i].text;
+        const isPara = t === PARAGRAPH_SENTINEL || t.startsWith('\uE000') || t.includes('PARA');
+        // Skip paragraph sentinel tokens entirely from labels and grouping
+        if (!isPara) {
+          parts.push(t);
+          // Only add to grouping if there is a corresponding metadata index
+          if (metadata[metadataIndex]) {
+            runIndices.push(metadataIndex);
+          }
+        }
         metadataIndex += 1;
         i += 1;
       }
       i -= 1;
-      const endIndex = metadataIndex - 1;
-      const groupId = `${groupPrefix}-${startIndex}-${endIndex}`;
-      runIndices.forEach((idx) => tokenIndexToGroupId.set(idx, groupId));
       const label = parts.join(' ').trim();
-      items.push({ value: groupId, label: label || '(…)', pageNumber });
+      if (label.length > 0 && runIndices.length > 0) {
+        const startIndexForId = runIndices[0];
+        const endIndexForId = runIndices[runIndices.length - 1];
+        const groupId = `${groupPrefix}-${startIndexForId}-${endIndexForId}`;
+        runIndices.forEach((idx) => tokenIndexToGroupId.set(idx, groupId));
+        items.push({ value: groupId, label, pageNumber });
+      }
       continue;
     }
     if (token.type !== (targetType === 'added' ? 'removed' : 'added')) {
diff --git a/frontend/src/components/tools/compare/hooks/useComparePanZoom.ts b/frontend/src/components/tools/compare/hooks/useComparePanZoom.ts
index 288d057e3..39bf7bf59 100644
--- a/frontend/src/components/tools/compare/hooks/useComparePanZoom.ts
+++ b/frontend/src/components/tools/compare/hooks/useComparePanZoom.ts
@@ -29,6 +29,13 @@ interface ScrollLinkDelta {
   horizontal: number;
 }
 
+// Pixel-based anchors captured when linking scroll, to preserve the
+// visual offset between panes and avoid an initial snap.
+interface ScrollLinkAnchors {
+  deltaPixelsBaseToComp: number;
+  deltaPixelsCompToBase: number;
+}
+
 interface PanDragState {
   active: boolean;
   source: Pane | null;
@@ -93,6 +100,10 @@ export const useComparePanZoom = ({
   const comparisonScrollRef = useRef<HTMLDivElement>(null);
   const isSyncingRef = useRef(false);
   const scrollLinkDeltaRef = useRef<ScrollLinkDelta>({ vertical: 0, horizontal: 0 });
+  const scrollLinkAnchorsRef = useRef<ScrollLinkAnchors>({
+    deltaPixelsBaseToComp: 0,
+    deltaPixelsCompToBase: 0,
+  });
   const [isScrollLinked, setIsScrollLinked] = useState(true);
   const [isPanMode, setIsPanMode] = useState(false);
   const panDragRef = useRef<PanDragState>({
@@ -328,12 +339,16 @@ export const useComparePanZoom = ({
       lastActivePaneRef.current = source === baseScrollRef.current ? 'base' : 'comparison';
 
       const sourceIsBase = source === baseScrollRef.current;
-      const deltaV = scrollLinkDeltaRef.current.vertical;
 
       const targetVerticalRange = Math.max(1, target.scrollHeight - target.clientHeight);
       const mappedTop = mapScrollTopBetweenPanes(source.scrollTop, sourceIsBase);
-      const offset = deltaV * targetVerticalRange;
-      const desiredTop = Math.max(0, Math.min(targetVerticalRange, mappedTop + (sourceIsBase ? offset : -offset)));
+
+      // Use pixel anchors captured at link time to preserve offset
+      const deltaPx = sourceIsBase
+        ? scrollLinkAnchorsRef.current.deltaPixelsBaseToComp
+        : scrollLinkAnchorsRef.current.deltaPixelsCompToBase;
+
+      const desiredTop = Math.max(0, Math.min(targetVerticalRange, mappedTop + deltaPx));
 
       isSyncingRef.current = true;
       target.scrollTop = desiredTop;
@@ -623,6 +638,7 @@ export const useComparePanZoom = ({
     const compEl = comparisonScrollRef.current;
     if (!baseEl || !compEl) {
       scrollLinkDeltaRef.current = { vertical: 0, horizontal: 0 };
+      scrollLinkAnchorsRef.current = { deltaPixelsBaseToComp: 0, deltaPixelsCompToBase: 0 };
       return;
     }
     const baseVMax = Math.max(1, baseEl.scrollHeight - baseEl.clientHeight);
@@ -639,10 +655,19 @@ export const useComparePanZoom = ({
       vertical: compV - baseV,
       horizontal: compH - baseH,
     };
-  }, []);
+
+    // Capture pixel anchors in mapped space
+    const mappedBaseToComp = mapScrollTopBetweenPanes(baseEl.scrollTop, true);
+    const mappedCompToBase = mapScrollTopBetweenPanes(compEl.scrollTop, false);
+    scrollLinkAnchorsRef.current = {
+      deltaPixelsBaseToComp: compEl.scrollTop - mappedBaseToComp,
+      deltaPixelsCompToBase: baseEl.scrollTop - mappedCompToBase,
+    };
+  }, [mapScrollTopBetweenPanes]);
 
   const clearScrollLinkDelta = useCallback(() => {
     scrollLinkDeltaRef.current = { vertical: 0, horizontal: 0 };
+    scrollLinkAnchorsRef.current = { deltaPixelsBaseToComp: 0, deltaPixelsCompToBase: 0 };
   }, []);
 
   const zoomLimits = useMemo(() => ({ min: ZOOM_MIN, max: ZOOM_MAX, step: ZOOM_STEP }), []);
diff --git a/frontend/src/tools/Compare.tsx b/frontend/src/tools/Compare.tsx
index bb0663c55..def35e21d 100644
--- a/frontend/src/tools/Compare.tsx
+++ b/frontend/src/tools/Compare.tsx
@@ -2,6 +2,7 @@ import { useCallback, useEffect, useMemo, useRef } from 'react';
 import { useTranslation } from 'react-i18next';
 import CompareRoundedIcon from '@mui/icons-material/CompareRounded';
 import { Box, Group, Stack, Text, Button } from '@mantine/core';
+import { Tooltip } from '../components/shared/Tooltip';
 import { createToolFlow } from '../components/tools/shared/createToolFlow';
 import { useBaseTool } from '../hooks/tools/shared/useBaseTool';
 import { BaseToolProps, ToolComponent } from '../types/tool';
@@ -22,6 +23,7 @@ import type { StirlingFile } from '../types/fileContext';
 import DocumentThumbnail from '../components/shared/filePreview/DocumentThumbnail';
 import './compareTool.css';
 import type { CompareWorkbenchData } from '../types/compareWorkbench';
+import FitText from '../components/shared/FitText';
 
 const CUSTOM_VIEW_ID = 'compareWorkbenchView';
 const CUSTOM_WORKBENCH_ID = 'custom:compareWorkbenchView' as const;
@@ -234,9 +236,14 @@ const Compare = (props: BaseToolProps) => {
               <DocumentThumbnail file={stub ?? null} thumbnail={stub?.thumbnailUrl || null} />
             </Box>
             <Stack gap={4} className="compare-tool__details">
-              <Text fw={600} truncate>
-                {stub?.name}
-              </Text>
+              <Tooltip content={stub?.name || ''} position="top" arrow>
+                <FitText 
+                  text={stub?.name || ''} 
+                  minimumFontScale={0.5} 
+                  lines={2}
+                  style={{ fontWeight: 600 }}
+                />
+              </Tooltip>
               {meta && (
                 <Text size="sm" c="dimmed">
                   {meta}