My Pre (on both 1.4.5 and 2.1.0) just experiences the occasional "alarm list disappearing" trick, but is otherwise fine. My girlfriend has a Veer, and that's got some strange alarm behavior!
Often, her Veer's alarms won't go off unless the screen is on.
Let's say we set an alarm for 7:00. 7:05 comes around, and the phone hasn't made a sound. If you press the power button to wake it, the alarm will then start going off.
Hers is a stock phone - the only 3rd party application she installed on it was Nyan Cat. Well after this problem came about, she let me enable developer mode, install Preware, Save/Restore, White Pages, and the dialer patch for white pages. That's it for not-built-into-the-webOS-Doctor software, and the problem showed up before and after.
We work around it by putting the phone on the Touchstone at night, but it's a pretty ridiculous issue to have.