I use BigJ's Alarm Clock, and noticed that it did not wake up the phone to sound the alarm this morning. I'll test more to make sure I can recreate that.
Loving your ROM's J, keep it up!
(I'm using the 1.0r kitchen.)
Update: The alarm app locked up on me when I tried to change the settings just now. The rest of the pda seemed ok, just the alarm app was messed up. As soon as I soft reset, my alarm started going off. I set a new alarm and the phone did wake up for the alarm this time.