diff --git a/desktop/src/shared/profiling/drift.ts b/desktop/src/shared/profiling/drift.ts
index 098874b0a..72e0af38d 100644
--- a/desktop/src/shared/profiling/drift.ts
+++ b/desktop/src/shared/profiling/drift.ts
@@ -1,13 +1,26 @@
-// Temporary renderer profiling harness (never merges) — event-loop drift math.
+// Temporary renderer profiling harness (never merges) — sampling math.
 //
-// WebKit exposes no Long Tasks API, so main-thread stalls are inferred from
-// timer drift: a timer armed for `intervalMs` that fires late by more than
-// `thresholdMs` means the main thread was blocked for roughly that overage.
+// Pure, deterministic decision helpers for the two DOM-driven probes so the
+// harness wiring stays thin and the judgement is unit-testable without loading
+// the harness's Tauri/store imports:
+//   - main-thread stalls, inferred from timer drift (WebKit has no Long Tasks
+//     API): a timer armed for `intervalMs` that fires late by more than
+//     `thresholdMs` means the main thread was blocked for roughly that overage;
+//   - input latency, split into the pre-dispatch queue delay and the
+//     post-receipt paint delay.
 
 /** Default sampling interval for the drift timer. */
 export const DRIFT_INTERVAL_MS = 500;
 /** Report a stall only when drift exceeds this — filters normal scheduler jitter. */
 export const DRIFT_THRESHOLD_MS = 50;
+/** Record an input event only when its total felt latency reaches this. */
+export const INPUT_LATENCY_MIN_MS = 100;
+/**
+ * Largest plausible pre-dispatch age. A larger (or negative) `event.timeStamp`
+ * → `performance.now()` delta means the two are on different clock bases, so
+ * the queue figure is dropped rather than trusted.
+ */
+export const MAX_INPUT_QUEUED_MS = 60_000;
 
 /**
  * Overage of an observed timer fire versus its expected fire time.
@@ -24,3 +37,51 @@ export function computeDrift(
   const drift = observed - expected;
   return drift > thresholdMs ? drift : null;
 }
+
+/**
+ * Judge one drift interval and re-arm the baseline.
+ *
+ * `eligible` is false whenever the interval did not both begin and end in the
+ * visible, focused foreground (a hidden/occluded/asleep webview defers timers,
+ * and that deferral must never be attributed to a main-thread block). An
+ * ineligible interval records nothing but still re-arms `armedAt` to `observed`
+ * so the first foreground interval after a return cannot manufacture a phantom
+ * stall from the accumulated background gap.
+ */
+export function nextStallSample(
+  armedAt: number,
+  observed: number,
+  eligible: boolean,
+  intervalMs: number = DRIFT_INTERVAL_MS,
+  thresholdMs: number = DRIFT_THRESHOLD_MS,
+): { dur: number | null; armedAt: number } {
+  const dur = eligible
+    ? computeDrift(observed, armedAt + intervalMs, thresholdMs)
+    : null;
+  return { dur, armedAt: observed };
+}
+
+/**
+ * Split an input event's felt latency into its two additive parts and decide
+ * whether it clears the recording threshold.
+ *
+ * `latency` is `paintedAt - receivedAt`: the capture-phase listener's receipt
+ * (a `performance.now()` read taken synchronously in the listener) to the next
+ * painted frame. `queued` is `receivedAt - eventTimeStamp`: the pre-dispatch
+ * delay — the dominant signal when a busy main thread stalls event dispatch —
+ * or `null` when that delta is implausible (a clock-basis mismatch). The event
+ * is recorded when the total felt latency (`latency + queued`) reaches `minMs`.
+ */
+export function classifyInput(
+  eventTimeStamp: number,
+  receivedAt: number,
+  paintedAt: number,
+  minMs: number = INPUT_LATENCY_MIN_MS,
+): { latency: number; queued: number | null } | null {
+  const latency = paintedAt - receivedAt;
+  const rawQueued = receivedAt - eventTimeStamp;
+  const queued =
+    rawQueued >= 0 && rawQueued <= MAX_INPUT_QUEUED_MS ? rawQueued : null;
+  const felt = latency + (queued ?? 0);
+  return felt >= minMs ? { latency, queued } : null;
+}
diff --git a/desktop/src/shared/profiling/harness.test.mjs b/desktop/src/shared/profiling/harness.test.mjs
index ecb8e3f89..5efa4f077 100644
--- a/desktop/src/shared/profiling/harness.test.mjs
+++ b/desktop/src/shared/profiling/harness.test.mjs
@@ -10,7 +10,12 @@
 import assert from "node:assert/strict";
 import { describe, it } from "node:test";
 
-import { computeDrift, DRIFT_THRESHOLD_MS } from "@/shared/profiling/drift.ts";
+import {
+  classifyInput,
+  computeDrift,
+  DRIFT_THRESHOLD_MS,
+  nextStallSample,
+} from "@/shared/profiling/drift.ts";
 import { ProfileRecorder, RING_CAPACITY } from "@/shared/profiling/recorder.ts";
 
 function fixedClock() {
@@ -37,6 +42,56 @@ describe("computeDrift", () => {
   });
 });
 
+describe("nextStallSample", () => {
+  it("records a real overrun in an eligible (foreground) interval", () => {
+    // armed at 1000, interval 500 → expected 1500; observed 1800 → 300 overrun.
+    const { dur, armedAt } = nextStallSample(1000, 1800, true, 500, 50);
+    assert.equal(dur, 300);
+    assert.equal(armedAt, 1800);
+  });
+
+  it("suppresses the record but re-arms the baseline when ineligible", () => {
+    // A hidden/blurred interval defers the timer arbitrarily; the huge gap must
+    // not be scored, but armedAt must advance so the next interval is clean.
+    const { dur, armedAt } = nextStallSample(1000, 60_000, false, 500, 50);
+    assert.equal(dur, null);
+    assert.equal(armedAt, 60_000);
+  });
+
+  it("cannot manufacture a phantom stall on the interval after a return", () => {
+    // Background interval [1000, 60000] re-armed to 60000 with no record.
+    const background = nextStallSample(1000, 60_000, false, 500, 50);
+    // First foreground interval fires on time from the re-armed baseline.
+    const resumed = nextStallSample(background.armedAt, 60_500, true, 500, 50);
+    assert.equal(resumed.dur, null);
+  });
+});
+
+describe("classifyInput", () => {
+  it("splits felt latency into paint delay and pre-dispatch queue", () => {
+    // event@100, received@250 (queued 150), painted@300 (latency 50) → felt 200.
+    const result = classifyInput(100, 250, 300);
+    assert.deepEqual(result, { latency: 50, queued: 150 });
+  });
+
+  it("drops the queue figure when the clock basis is implausible", () => {
+    // event.timeStamp on a different origin: received - timeStamp is negative.
+    const result = classifyInput(9_999_999, 250, 400);
+    assert.deepEqual(result, { latency: 150, queued: null });
+  });
+
+  it("returns null when total felt latency is under threshold", () => {
+    // queued 10 + latency 20 = 30ms felt, below the 100ms floor.
+    assert.equal(classifyInput(100, 110, 130), null);
+  });
+
+  it("uses only paint latency toward the threshold when queue is implausible", () => {
+    // queued dropped (negative); latency 120 alone clears the floor.
+    const result = classifyInput(9_999_999, 250, 370);
+    assert.deepEqual(result, { latency: 120, queued: null });
+  });
+});
+
 describe("ProfileRecorder ring buffer", () => {
   it("bounds the buffer at RING_CAPACITY, dropping oldest", async () => {
     const rec = new ProfileRecorder("session-1", async () => {}, fixedClock());
diff --git a/desktop/src/shared/profiling/harness.ts b/desktop/src/shared/profiling/harness.ts
index 7bf287ece..4795cac68 100644
--- a/desktop/src/shared/profiling/harness.ts
+++ b/desktop/src/shared/profiling/harness.ts
@@ -2,7 +2,8 @@
 //
 // One always-on harness that ring-buffers timing records and flushes JSONL to
 // `<app-data>/profiling/session-<ts>.jsonl`. Four probes:
-//   1. main-thread stalls (timer drift) + input latency (down → next paint)
+//   1. main-thread stalls (timer drift, foreground-only) + input latency
+//      (receipt → next paint, with pre-dispatch queue delay split out)
 //   2. Tauri IPC duration/outcome + a >10s pending-invoke watchdog (deadlocks)
 //   3. relay REQ→EOSE (history fetch) and publish send→ack round-trips
 //   4. periodic accumulator census (observer store, query cache, DOM nodes)
@@ -18,8 +19,8 @@ import { getObserverStoreCensus } from "@/features/agents/observerRelayStore";
 import { relayClient } from "@/shared/api/relayClient";
 import {
   DRIFT_INTERVAL_MS,
-  DRIFT_THRESHOLD_MS,
-  computeDrift,
+  classifyInput,
+  nextStallSample,
 } from "@/shared/profiling/drift";
 import {
   FLUSH_INTERVAL_MS,
@@ -29,7 +30,6 @@ import {
 const CENSUS_INTERVAL_MS = 120_000;
 const PENDING_INVOKE_MS = 10_000;
 const PENDING_SCAN_MS = 5_000;
-const INPUT_LATENCY_MIN_MS = 100;
 
 // RelayClient methods whose resolution marks a REQ→EOSE round-trip (history
 // fetches resolve when the relay sends EOSE) versus a publish send→ack
@@ -137,35 +137,60 @@ function installIpcProbe(rec: ProfileRecorder): void {
   }, PENDING_SCAN_MS);
 }
 
+function isForeground(): boolean {
+  return document.visibilityState === "visible" && document.hasFocus();
+}
+
 function installStallProbe(rec: ProfileRecorder): void {
   let armedAt = performance.now();
+  // An interval only counts if the document stayed visible+focused for its
+  // whole span. Any blur/hide between arms taints the current interval so a
+  // background gap is never scored as a main-thread block.
+  let continuousForeground = isForeground();
+  const taint = () => {
+    continuousForeground = false;
+  };
+  document.addEventListener("visibilitychange", taint);
+  window.addEventListener("blur", taint);
   window.setInterval(() => {
     const observed = performance.now();
-    const drift = computeDrift(
-      observed,
-      armedAt + DRIFT_INTERVAL_MS,
-      DRIFT_THRESHOLD_MS,
-    );
-    if (drift !== null) {
-      rec.record({ type: "stall", dur: drift });
+    const eligible = continuousForeground && isForeground();
+    const sample = nextStallSample(armedAt, observed, eligible);
+    if (sample.dur !== null) {
+      rec.record({ type: "stall", dur: sample.dur });
     }
-    armedAt = observed;
+    armedAt = sample.armedAt;
+    // Re-arm cleanly: the next interval is continuous only if we are in the
+    // foreground right now.
+    continuousForeground = isForeground();
   }, DRIFT_INTERVAL_MS);
 }
 
 function installInputProbe(rec: ProfileRecorder): void {
   const onInput = (kind: "keydown" | "pointerdown") => (event: Event) => {
-    const start = event.timeStamp;
+    // Capture the harness's own receipt clock synchronously, in the listener,
+    // so `latency` is receipt → next painted frame on a single clock basis.
+    const receivedAt = performance.now();
+    const eventTimeStamp = event.timeStamp;
     requestAnimationFrame(() =>
       requestAnimationFrame(() => {
-        const latency = performance.now() - start;
-        if (latency >= INPUT_LATENCY_MIN_MS) {
-          rec.record({ type: "input", kind, latency });
+        const result = classifyInput(
+          eventTimeStamp,
+          receivedAt,
+          performance.now(),
+        );
+        if (result !== null) {
+          rec.record({
+            type: "input",
+            kind,
+            latency: result.latency,
+            queued: result.queued,
+          });
         }
       }),
     );
   };
-  // Capture phase so the timestamp precedes app handlers.
+  // Capture phase so the receipt clock precedes app handlers.
   window.addEventListener("keydown", onInput("keydown"), {
     capture: true,
     passive: true,
diff --git a/desktop/src/shared/profiling/types.ts b/desktop/src/shared/profiling/types.ts
index 54d789ff0..13a1c6044 100644
--- a/desktop/src/shared/profiling/types.ts
+++ b/desktop/src/shared/profiling/types.ts
@@ -24,8 +24,14 @@ export type StallRecord = ProfileEnvelope & {
 export type InputRecord = ProfileEnvelope & {
   type: "input";
   kind: "keydown" | "pointerdown";
-  /** Event timestamp → next painted frame, ms. */
+  /** Capture-listener receipt → next painted frame, ms (single-clock). */
   latency: number;
+  /**
+   * Pre-dispatch delay: `event.timeStamp` → capture-listener receipt, ms.
+   * `null` when that delta is implausible (a cross-clock basis mismatch).
+   * Total felt latency is `latency + (queued ?? 0)`.
+   */
+  queued: number | null;
 };
 
 export type IpcRecord = ProfileEnvelope & {