http://ea.jetbrains.com/browser/ea_problems/17701

platform/vcs-impl/src/com/intellij/lifecycle/PeriodicalTasksCloser.java

@@ -56,12 +56,13 @@ public class PeriodicalTasksCloser implements ProjectManagerListener {
     return ServiceManager.getService(project, PeriodicalTasksCloser.class);
   }
 
-  public void register(final String name, final Runnable runnable) {
+  public boolean register(final String name, final Runnable runnable) {
     synchronized (ourLock) {
       if (Boolean.FALSE.equals(myStates.get(myProject))) {
-        return;
+        return false;
       }
       myInterrupters.add(new Pair<String, Runnable>(name, runnable));
+      return true;
     }
   }       
 

platform/vcs-impl/src/com/intellij/lifecycle/SlowlyClosingAlarm.java

@@ -80,7 +80,7 @@ public class SlowlyClosingAlarm implements AtomicSectionsAware, Disposable {
     myLock = new Object();
     myFutureList = new ArrayList<Future<?>>();
     Disposer.register(project, this);
-    PeriodicalTasksCloser.getInstance(project).register(name, new Runnable() {
+    myDisposeStarted = ! PeriodicalTasksCloser.getInstance(project).register(name, new Runnable() {
       public void run() {
         waitAndInterrupt(ProgressManager.getInstance().getProgressIndicator());
       }