diff --git a/services/runner/src/engines/sandbox_agent/acp-interactions.ts b/services/runner/src/engines/sandbox_agent/acp-interactions.ts
index 3f04a0eecb..b0f8a3d5fd 100644
--- a/services/runner/src/engines/sandbox_agent/acp-interactions.ts
+++ b/services/runner/src/engines/sandbox_agent/acp-interactions.ts
@@ -35,6 +35,7 @@ export interface PiToolSpecMeta {
 }
 
 export interface AttachPermissionResponderInput {
+  onPermissionRequestStarted?: (toolCallId: string) => void;
   session: any;
   run: {
     emitEvent: (event: AgentEvent) => void;
@@ -125,6 +126,7 @@ export function attachPermissionResponder({
   onPause,
   log,
   onPausedToolCall,
+  onPermissionRequestStarted,
   onAllowedExecution,
   onAnsweredDeny,
   onNonParkablePause,
@@ -367,6 +369,9 @@ export function attachPermissionResponder({
           }),
       );
     }
+    if (envelope.toolCallId) {
+      onPermissionRequestStarted?.(envelope.toolCallId);
+    }
     const verdict = await responder.onPermission({
       id,
       availableReplies,
@@ -462,6 +467,11 @@ export function attachPermissionResponder({
       return;
     }
 
+    const toolCallId = stringValue(toolCall?.toolCallId);
+    if (toolCallId) {
+      onPermissionRequestStarted?.(toolCallId);
+    }
+
     const verdict = await responder.onPermission({
       id,
       availableReplies,
@@ -476,7 +486,7 @@ export function attachPermissionResponder({
       id,
       verdict.kind,
       availableReplies,
-      stringValue(toolCall?.toolCallId),
+      toolCallId,
       verdict.interactionToken,
     );
   }
@@ -635,4 +645,4 @@ function clientToolReply(
 
 function errorMessage(err: unknown): string {
   return err instanceof Error ? err.message : String(err);
-}
+}
\ No newline at end of file
diff --git a/services/runner/src/engines/sandbox_agent/pause.ts b/services/runner/src/engines/sandbox_agent/pause.ts
index fe7b2dc23e..9f18bf6f62 100644
--- a/services/runner/src/engines/sandbox_agent/pause.ts
+++ b/services/runner/src/engines/sandbox_agent/pause.ts
@@ -13,6 +13,7 @@ const EVENT_DRAIN_MAX_TICKS = 6;
 
 export class PendingApprovalPauseController {
   private pendingApproval = false;
+  private readonly inFlightPermissionToolCallIds = new Set<string>();
   private readonly pausedToolCallIds = new Set<string>();
   private readonly allowedExecutionToolCallIds = new Set<string>();
   private readonly answeredDenyToolCallIds = new Set<string>();
@@ -72,23 +73,40 @@ export class PendingApprovalPauseController {
    * last word for the call this turn. Later harness frames for the same id are teardown artifacts
    * from cancellation/session disposal and must not reach the event stream.
    */
-  markPausedToolCall(toolCallId: string): void {
-    if (!toolCallId) return;
-    const added = !this.pausedToolCallIds.has(toolCallId);
-    this.pausedToolCallIds.add(toolCallId);
-    // A late gate must extend terminalization long enough for its paused classification to land.
-    if (this.pendingApproval && added) this.gateClassificationVersion += 1;
+ markPausedToolCall(toolCallId: string): void {
+  if (!toolCallId) return;
+
+  this.inFlightPermissionToolCallIds.delete(toolCallId);
+
+  const added = !this.pausedToolCallIds.has(toolCallId);
+  this.pausedToolCallIds.add(toolCallId);
+
+  if (this.pendingApproval && added) {
+    this.gateClassificationVersion += 1;
+  }
+}
+
+  markPermissionRequestStarted(toolCallId: string): void {
+    if (toolCallId) {
+      this.inFlightPermissionToolCallIds.add(toolCallId);
+    }
   }
 
+  isInFlightPermission(toolCallId: string | undefined): boolean {
+    return toolCallId !== undefined && this.inFlightPermissionToolCallIds.has(toolCallId);
+  }
   isPausedToolCall(toolCallId: string | undefined): boolean {
     return toolCallId !== undefined && this.pausedToolCallIds.has(toolCallId);
   }
 
   /** Record that this turn answered allow for the call, so pause cleanup preserves its result. */
   markAllowedExecution(toolCallId: string): void {
-    if (!toolCallId) return;
-    this.allowedExecutionToolCallIds.add(toolCallId);
-  }
+  if (!toolCallId) return;
+
+  this.inFlightPermissionToolCallIds.delete(toolCallId);
+
+  this.allowedExecutionToolCallIds.add(toolCallId);
+}
 
   /** Record an answered deny so its authoritative failed frame survives a sibling pause. */
   markAnsweredDeny(toolCallId: string): void {
diff --git a/services/runner/src/engines/sandbox_agent/run-turn.ts b/services/runner/src/engines/sandbox_agent/run-turn.ts
index d9b328f841..047e60e075 100644
--- a/services/runner/src/engines/sandbox_agent/run-turn.ts
+++ b/services/runner/src/engines/sandbox_agent/run-turn.ts
@@ -414,7 +414,9 @@ export async function runTurn(
           if (pause.active) {
             run.settleOpenToolCalls(
               (id) =>
-                pause.isPausedToolCall(id) || pause.isAllowedExecution(id),
+                pause.isPausedToolCall(id) || 
+            pause.isAllowedExecution(id) || 
+            pause.isInFlightPermission(id),
               TOOL_NOT_EXECUTED_PAUSED,
             );
           }
@@ -582,6 +584,7 @@ export async function runTurn(
       serverPermissions,
       log: logger,
       onPause: () => pause.pause(),
+      onPermissionRequestStarted: (id) => pause.markPermissionRequestStarted(id),
       onPausedToolCall: (id) => pause.markPausedToolCall(id),
       onAllowedExecution: (id) => pause.markAllowedExecution(id),
       onAnsweredDeny: (id) => pause.markAnsweredDeny(id),