diff --git a/.github/scripts/agents_pr_meta_keepalive.js b/.github/scripts/agents_pr_meta_keepalive.js
index 7a219753..10eab2c8 100644
--- a/.github/scripts/agents_pr_meta_keepalive.js
+++ b/.github/scripts/agents_pr_meta_keepalive.js
@@ -240,6 +240,11 @@ function extractIssueNumberFromPull(pull) {
     if (match.index > 0 && /\w/.test(bodyText[match.index - 1])) {
       continue;
     }
+    // Skip non-issue refs like "Run #123", "run #123", "attempt #2"
+    const preceding = bodyText.slice(Math.max(0, match.index - 20), match.index);
+    if (/\b(?:run|attempt|step|job|check|task|version|v)\s*$/i.test(preceding)) {
+      continue;
+    }
     candidates.push(match[1]);
   }
 
diff --git a/.github/scripts/agents_pr_meta_update_body.js b/.github/scripts/agents_pr_meta_update_body.js
index ec9a585a..3e987c10 100644
--- a/.github/scripts/agents_pr_meta_update_body.js
+++ b/.github/scripts/agents_pr_meta_update_body.js
@@ -404,7 +404,7 @@ function parseCheckboxStates(block) {
     if (inCodeBlock) {
       continue;
     }
-    const match = line.match(/^- \[(x| )\]\s*(.+)$/i);
+    const match = line.match(/^\s*- \[(x| )\]\s*(.+)$/i);
     if (match) {
       const checked = match[1].toLowerCase() === 'x';
       const text = match[2].trim();
@@ -461,12 +461,13 @@ function mergeCheckboxStates(newContent, existingStates) {
       updated.push(line);
       continue;
     }
-    const match = line.match(/^- \[( )\]\s*(.+)$/);
+    const match = line.match(/^(\s*)- \[( )\]\s*(.+)$/);
     if (match) {
-      const text = match[2].trim();
+      const indent = match[1];
+      const text = match[3].trim();
       const normalized = text.replace(/^-\s*/, '').trim().toLowerCase();
       if (existingStates.has(normalized)) {
-        updated.push(`- [x] ${text}`);
+        updated.push(`${indent}- [x] ${text}`);
         continue;
       }
     }