diff --git a/config/tsconfig.cli.json b/config/tsconfig.cli.json
index 0d278a1e854..a4df2dab4a9 100644
--- a/config/tsconfig.cli.json
+++ b/config/tsconfig.cli.json
@@ -21,6 +21,7 @@
     "../src/main/codex/codex-hook-identity.ts",
     "../src/main/codex/codex-hook-trust-grant.ts",
     "../src/main/codex/codex-managed-trust-reconciliation.ts",
+    "../src/main/codex/codex-process-exit-deadline.ts",
     "../src/main/codex/codex-trust-config-rollback.ts",
     "../src/main/codex/codex-trust-grant-host.ts",
     "../src/main/codex/codex-trust-grant-ledger.ts",
diff --git a/src/main/codex/codex-app-server-client.test.ts b/src/main/codex/codex-app-server-client.test.ts
index 82df78a57d2..5bb01ae5614 100644
--- a/src/main/codex/codex-app-server-client.test.ts
+++ b/src/main/codex/codex-app-server-client.test.ts
@@ -1,4 +1,4 @@
-import { afterEach, describe, expect, it } from 'vitest'
+import { afterEach, describe, expect, it, vi } from 'vitest'
 import { mkdtempSync, readFileSync, rmSync, writeFileSync, existsSync } from 'node:fs'
 import { tmpdir } from 'node:os'
 import { join } from 'node:path'
@@ -90,6 +90,7 @@ function writeFileSyncSafe(file, contents) { require('node:fs').writeFileSync(fi
 let tempRoots: string[] = []
 
 afterEach(() => {
+  vi.restoreAllMocks()
   for (const root of tempRoots) {
     rmSync(root, { recursive: true, force: true })
   }
@@ -149,6 +150,8 @@ function managedHook(key: string, trustStatus = 'untrusted'): StubHook {
 
 describe('runCodexHookTrustGrantSession', () => {
   it('grants and verifies exactly the expected managed entries', async () => {
+    const setTimeoutSpy = vi.spyOn(globalThis, 'setTimeout')
+    const clearTimeoutSpy = vi.spyOn(globalThis, 'clearTimeout')
     const keys = [
       '/home/a/.codex/hooks.json:session_start:0:0',
       '/home/a/.codex/hooks.json:stop:0:0'
@@ -191,6 +194,13 @@ describe('runCodexHookTrustGrantSession', () => {
     expect(written.edits[0].mergeStrategy).toBe('upsert')
     expect(Object.keys(written.edits[0].value).sort()).toEqual([...keys].sort())
     expect(written.reloadUserConfig).toBe(true)
+    // Why: the entry process waits on these handles after setting exitCode, so
+    // an uncleared grace timer adds its full delay to synchronous launch prep.
+    const timerHandles = setTimeoutSpy.mock.results.map(({ value }) => value)
+    expect(timerHandles).toHaveLength(2)
+    expect(clearTimeoutSpy.mock.calls.map(([handle]) => handle)).toEqual(
+      expect.arrayContaining(timerHandles)
+    )
   })
 
   it('skips config/batchWrite when every expected entry is already trusted', async () => {
diff --git a/src/main/codex/codex-app-server-client.ts b/src/main/codex/codex-app-server-client.ts
index 0273893fcc8..ab5dced425c 100644
--- a/src/main/codex/codex-app-server-client.ts
+++ b/src/main/codex/codex-app-server-client.ts
@@ -1,5 +1,6 @@
 import { spawn, type ChildProcessWithoutNullStreams } from 'node:child_process'
 import { normalizeHookTrustKeyForLookup } from './config-toml-trust'
+import { waitForProcessExitUntil } from './codex-process-exit-deadline'
 
 // Why: Codex gates hooks on a `trusted_hash` it computes from a private
 // canonical-JSON identity. Orca used to replicate that algorithm
@@ -363,11 +364,10 @@ export async function runCodexHookTrustGrantSession(
     if (!exited) {
       // Why: the server exits promptly on stdin EOF; the grace period only
       // bounds a wedged child before the guaranteed SIGKILL reap.
-      const grace = new Promise<void>((resolve) => setTimeout(resolve, 1500))
-      await Promise.race([exitPromise, grace])
+      await waitForProcessExitUntil(exitPromise, 1500)
       if (!exited) {
         child.kill('SIGKILL')
-        await Promise.race([exitPromise, new Promise<void>((resolve) => setTimeout(resolve, 1000))])
+        await waitForProcessExitUntil(exitPromise, 1000)
       }
     }
     clearTimeout(deadline)
diff --git a/src/main/codex/codex-config-mirror.test.ts b/src/main/codex/codex-config-mirror.test.ts
index 5022fff5cc0..4b425e2e2ef 100644
--- a/src/main/codex/codex-config-mirror.test.ts
+++ b/src/main/codex/codex-config-mirror.test.ts
@@ -268,6 +268,9 @@ describe('syncSystemConfigIntoManagedCodexHome', () => {
       [
         'model = "runtime-model"',
         '',
+        '[hooks.state]',
+        '# runtime-owned parent',
+        '',
         '[hooks.state."runtime-hooks:stop:0:0"]',
         'enabled = false',
         'trusted_hash = "sha256:runtime"',
@@ -286,6 +289,9 @@ describe('syncSystemConfigIntoManagedCodexHome', () => {
       [
         'model = "system-model"',
         '',
+        '[hooks.state]',
+        '# system-owned parent',
+        '',
         '[projects."/repo"] # explicit revocation',
         'trust_level = "untrusted"',
         '',
@@ -310,6 +316,8 @@ describe('syncSystemConfigIntoManagedCodexHome', () => {
     expect(runtimeConfig).toContain('[projects."/system-only"]')
     expect(runtimeConfig).toContain('[hooks.state."runtime-hooks:stop:0:0"]')
     expect(runtimeConfig).not.toContain('[hooks.state."system-hooks:stop:0:0"]')
+    expect(runtimeConfig).toContain('# runtime-owned parent')
+    expect(runtimeConfig).not.toContain('# system-owned parent')
     expect(runtimeConfig).toContain('trust_level = "untrusted"')
     expect(runtimeConfig.match(/\[projects\."\/repo"\]/g)?.length).toBe(1)
   })
diff --git a/src/main/codex/codex-config-mirror.ts b/src/main/codex/codex-config-mirror.ts
index e6ca4c0b834..26933c1ba02 100644
--- a/src/main/codex/codex-config-mirror.ts
+++ b/src/main/codex/codex-config-mirror.ts
@@ -275,7 +275,10 @@ function isRuntimePreservedTomlSection(header: string): boolean {
 }
 
 function isRuntimeHookTrustTomlSection(header: string): boolean {
-  return header.trimStart().startsWith('[hooks.state.')
+  const trimmed = header.trim()
+  // Why: Codex's config writer materializes the parent table on Windows. It is
+  // part of runtime-owned trust and must survive the next config mirror too.
+  return trimmed === '[hooks.state]' || trimmed.startsWith('[hooks.state.')
 }
 
 function isRuntimeProjectTomlSection(header: string): boolean {
diff --git a/src/main/codex/codex-process-exit-deadline.ts b/src/main/codex/codex-process-exit-deadline.ts
new file mode 100644
index 00000000000..d6eaf1eda2c
--- /dev/null
+++ b/src/main/codex/codex-process-exit-deadline.ts
@@ -0,0 +1,18 @@
+export async function waitForProcessExitUntil(
+  exitPromise: Promise<void>,
+  timeoutMs: number
+): Promise<void> {
+  let timer: ReturnType<typeof setTimeout> | undefined
+  const timeout = new Promise<void>((resolve) => {
+    timer = setTimeout(resolve, timeoutMs)
+  })
+  try {
+    await Promise.race([exitPromise, timeout])
+  } finally {
+    // Why: this runs in a short-lived entry; a live grace timer delays the
+    // parent spawnSync even after the app-server process has already exited.
+    if (timer !== undefined) {
+      clearTimeout(timer)
+    }
+  }
+}
diff --git a/src/main/codex/hook-service-trust-grant.test.ts b/src/main/codex/hook-service-trust-grant.test.ts
index 4c51040fc38..c308fde1cc0 100644
--- a/src/main/codex/hook-service-trust-grant.test.ts
+++ b/src/main/codex/hook-service-trust-grant.test.ts
@@ -7,6 +7,7 @@ import { wrapPosixHookCommand } from '../agent-hooks/installer-utils'
 import {
   computeTrustedHash,
   parseTrustKey,
+  readHookTrustEntries,
   upsertHookTrustEntries,
   type CodexTrustEntry
 } from './config-toml-trust'
@@ -160,7 +161,7 @@ describe('CodexHookService app-server trust grant lane', () => {
     })
   })
 
-  it('upgrades self-computed trust in place without duplicate tables', () => {
+  it('upgrades self-computed trust in place without duplicate logical entries', () => {
     prepareSystemHome()
     const service = new CodexHookService()
     process.env.ORCA_DISABLE_CODEX_TRUST_RPC = '1'
@@ -171,6 +172,9 @@ describe('CodexHookService app-server trust grant lane', () => {
 
     expect(service.install().state).toBe('installed')
     const upgraded = readFileSync(join(managedHome, 'config.toml'), 'utf-8')
+    // Why: the legacy Windows fallback intentionally writes slash variants;
+    // duplicate detection is about the normalized trust identity.
+    const upgradedEntries = readHookTrustEntries(join(managedHome, 'config.toml'))
     for (const eventLabel of [
       'session_start',
       'user_prompt_submit',
@@ -179,13 +183,12 @@ describe('CodexHookService app-server trust grant lane', () => {
       'post_tool_use',
       'stop'
     ]) {
-      const count = upgraded
-        .split('\n')
-        .filter(
-          (line) => line.startsWith('[hooks.state.') && line.includes(`:${eventLabel}:0:0`)
-        ).length
-      expect(count, `duplicate trust tables for ${eventLabel}`).toBe(1)
+      const count = [...upgradedEntries.keys()].filter((key) =>
+        key.endsWith(`:${eventLabel}:0:0`)
+      ).length
+      expect(count, `duplicate trust entries for ${eventLabel}`).toBe(1)
     }
+    expect(upgraded).toContain('sha256:codex-session_start')
   })
 
   it('leaves user trust byte-untouched while granting managed entries', () => {
diff --git a/src/main/codex/hook-service-wsl-runtime.test.ts b/src/main/codex/hook-service-wsl-runtime.test.ts
index cc887208f4c..c3d2ce9ca37 100644
--- a/src/main/codex/hook-service-wsl-runtime.test.ts
+++ b/src/main/codex/hook-service-wsl-runtime.test.ts
@@ -522,7 +522,11 @@ describe('Codex WSL runtime hook install app-server grant lane', () => {
     const basePlan = createTestPlan()
     writeFileSync(basePlan.configPath, '{"hooks":{}}\n', 'utf-8')
     writeFileSync(basePlan.tomlPath, '', 'utf-8')
+    let staleKeyExpectedRemoved: string | null = null
     const runner = vi.fn((request: CodexHookTrustGrantRequest) => {
+      if (staleKeyExpectedRemoved) {
+        expect(readHookTrustEntries(basePlan.tomlPath).has(staleKeyExpectedRemoved)).toBe(false)
+      }
       const entries = request.expectedTrustKeys.map((key) => {
         const parsed = parseTrustKey(key)!
         return {
@@ -557,6 +561,7 @@ describe('Codex WSL runtime hook install app-server grant lane', () => {
     const oldKey = computeTrustKey(
       getManagedTrustEntry(oldPlan, expectedManagedCommand(oldPlan.commandScriptPath))
     )
+    staleKeyExpectedRemoved = oldKey
 
     const newPlan = {
       ...basePlan,
diff --git a/src/main/codex/hook-service.ts b/src/main/codex/hook-service.ts
index b1b3ac7a3b2..ab680f6edca 100644
--- a/src/main/codex/hook-service.ts
+++ b/src/main/codex/hook-service.ts
@@ -842,6 +842,13 @@ function installManagedHooksIntoWslRuntime(
     // Why: a successful re-grant replaces the ledger. Keep the previous
     // records long enough to prove ownership of stale canonical-path keys.
     const previousLedgerHome = readCodexTrustGrantLedgerHomeForReconciliation(runtimeHomePath)
+    // Why: Codex's verified RPC write must be the final config mutation. A
+    // host-side rewrite after verification can race or invalidate that grant.
+    removeStaleWslRuntimeManagedHookTrustEntries(
+      plan.tomlPath,
+      trustEntries,
+      previousLedgerHome ? [previousLedgerHome] : []
+    )
     const grant = grantManagedCodexHookTrust({
       runtimeHomePath,
       tomlPath: plan.tomlPath,
@@ -849,17 +856,10 @@ function installManagedHooksIntoWslRuntime(
       managedEntries: trustEntries,
       host: { kind: 'wsl', distro: plan.wslDistro, linuxRuntimeHome: plan.linuxRuntimeHome }
     })
-    if (grant.lane === 'rpc') {
-      removeStaleWslRuntimeManagedHookTrustEntries(
-        plan.tomlPath,
-        grant.entries,
-        previousLedgerHome ? [previousLedgerHome] : []
-      )
-    } else {
+    if (grant.lane === 'fallback') {
       // Why: WSL runtime homes may carry user hook approvals we did not rebuild
       // here; only upsert Orca's entries instead of sweeping the whole source.
       upsertHookTrustEntries(plan.tomlPath, trustEntries)
-      removeStaleWslRuntimeManagedHookTrustEntries(plan.tomlPath, trustEntries)
     }
   } catch (error) {
     return {