diff --git a/src/plugins/diagnostics.ts b/src/plugins/diagnostics.ts
index a66e6fc6a..80030decd 100644
--- a/src/plugins/diagnostics.ts
+++ b/src/plugins/diagnostics.ts
@@ -49,20 +49,28 @@ export function formatPluginWarningsSummary(
 ): string | undefined {
   if (warnings.length === 0) return undefined;
 
+  // Deduped: one skill referenced by three plugins produces three warnings,
+  // and listing it three times makes the printed count disagree with the list.
+  const seenSkills = new Set<string>();
   const skillMisses: string[] = [];
+  let skillWarningCount = 0;
   for (const w of warnings) {
     const m = /skill "([^"]+)" referenced but not found/.exec(w);
-    if (m?.[1] !== undefined) skillMisses.push(m[1]);
+    if (m?.[1] === undefined) continue;
+    skillWarningCount += 1;
+    if (seenSkills.has(m[1])) continue;
+    seenSkills.add(m[1]);
+    skillMisses.push(m[1]);
   }
 
-  if (skillMisses.length > 0 && skillMisses.length === warnings.length) {
+  if (skillMisses.length > 0 && skillWarningCount === warnings.length) {
     const n = skillMisses.length;
     return `plugins: ${n} skill${n === 1 ? "" : "s"} missing: ${skillMisses.join(", ")}`;
   }
 
   if (skillMisses.length > 0) {
     const n = skillMisses.length;
-    const other = warnings.length - n;
+    const other = warnings.length - skillWarningCount;
     return `plugins: ${n} skill${n === 1 ? "" : "s"} missing (${skillMisses.join(", ")}); ${other} other warning${other === 1 ? "" : "s"}`;
   }
 
diff --git a/src/tui-opentui/runner-host.ts b/src/tui-opentui/runner-host.ts
index b98abd8d8..dff2cc83a 100644
--- a/src/tui-opentui/runner-host.ts
+++ b/src/tui-opentui/runner-host.ts
@@ -327,7 +327,7 @@ export async function mountRunnerHost(deps: RunnerHostDeps): Promise<RunnerHost>
     ...(deps.surfaces ?? {}),
     ...(host.openModels !== undefined ? { openModels: host.openModels } : {}),
     notify: (text) =>
-      appendStreamRow(host.shell, { role: "system", text, meta: "command" }),
+      appendStreamRow(host.shell, { role: "system", text }),
   }
 
   const refreshModels = (
diff --git a/src/tui/runner.ts b/src/tui/runner.ts
index 1a4d4ec6c..a88f418f8 100644
--- a/src/tui/runner.ts
+++ b/src/tui/runner.ts
@@ -150,6 +150,7 @@ import {
   setPromptRecognitionSource,
   setSentMessageHistory,
   setShellRunState,
+  surfaceStartupNotice,
 } from "../tui-opentui/shell.js";
 import {
   classifyAgentSendFailure,
@@ -1841,7 +1842,7 @@ export async function runTUI(initialConfig: Config): Promise<number> {
   };
 
   const systemRow = (text: string): void => {
-    appendStreamRow(host.shell, { role: "system", text, meta: "command" });
+    appendStreamRow(host.shell, { role: "system", text });
   };
 
   /** Settle the shell after a rejected send so the run does not look live. */
@@ -2370,9 +2371,12 @@ export async function runTUI(initialConfig: Config): Promise<number> {
       });
     });
 
-  // Surface fire-and-forget startup plugin diagnostics now that the shell has
-  // a transcript to write into (queued above, before `host` existed).
-  for (const notice of startupPluginNotices) systemRow(notice);
+  // Startup diagnostics ride the notice strip, not the transcript: an
+  // `appendStreamRow` here calls `clearLandingMark` and takes the whole landing
+  // hero with it — mark, the hints beside it, the composition — so a single
+  // plugin warning left a first run with no landing at all. Same reason
+  // CL-5618 routed MCP and hook failures here; this is the path it missed.
+  for (const notice of startupPluginNotices) surfaceStartupNotice(host.shell, notice);
 
   await host.waitUntilExit();
   // Quitting mid-stream is an abnormal end for the in-flight cycle: nothing