i think I have a little more information, and a related question.
If I mess around with the Chumby a little before the night alarm, the alarm will go off correctly. If it's a long time between messing around with it and the night-mode alarm, then the alarm won't go off. "Messing with" means going into the control panel either to play music or browse widgets in the current channel. My 'morning' alarms always go off, which is usually 6 hours from when I had to mess with control panel in order to manually put it into night mode.
So my question is could there be one or more widgets in my default channel which is using resources such that the clock/control panel timers are being thrown off?
I hope this helps; if there is anything you'd like me to try, let me know.