The login dialog was being opened with the main browser window as a parent in...

chrome/browser/dom_ui/new_tab_page_sync_handler.cc

Index: chrome/browser/dom_ui/new_tab_page_sync_handler.cc
===================================================================
--- chrome/browser/dom_ui/new_tab_page_sync_handler.cc	(revision 29327)
+++ chrome/browser/dom_ui/new_tab_page_sync_handler.cc	(working copy)
@@ -157,11 +157,11 @@
   DCHECK(sync_service_);
   if (sync_service_->HasSyncSetupCompleted()) {
     // User clicked the 'Login again' link to re-authenticate.
-    sync_service_->ShowLoginDialog();
+    sync_service_->ShowLoginDialog(NULL);
   } else {
     // User clicked the 'Start now' link to begin syncing.
     ProfileSyncService::SyncEvent(ProfileSyncService::START_FROM_NTP);
-    sync_service_->EnableForUser();
+    sync_service_->EnableForUser(NULL);
   }
 }