I installed JIT over over-clocked Tainted Vanilla a couple weeks ago, and at first everything seemed great--I was getting 5.1 Mflops on Linpack pretty consistently, and aside from the XDA app, everything seemed to work. From time to time an application would freeze and then force the phone to restart, but that was rare (every other day or so) and there didn't seem to be a pattern to it. But over time, the phone seemed to get less stable. For instance, (1) I would get an FC every time Gmail sync found new email and (2) Google Voice sync stopped working and (3) I lost the ability to do market updates. Eventually I figured out that the common thread was that all three operations updated the notification bar. And the Gmail app in particular seemed to fail as it tried to update the bar -- because it actually retrieved the incoming messages before FC'ing.
Eventually I backed out the JIT update and went back to plain old Tainted Vanilla, but I miss the JIT performance. Has anyone else noticed issues with the notification bar and JIT?