Yeah the "Maize" clock widget at first seemed like it might be causing some of the issues with my phone's alarm, not sure what it really was. But I wanted to keep it on my phone because it's so nice looking IMO and I can still see my backgrounds. After I messed with the settings a bit and tried setting it to show the "Thursday, October 7th" display and have "touching" the clock on the homepage set it so it takes it to the alarm, it seemed to stop happening.
The Maize one might be REALLY "connected" to the phone's ACTUAL clock (or I would wonder why it has those options to control the phone's clock and calendar if it wasn't); which is why if a task killer kills the Maize clock at screen timeout, it might effect the phone's built in clock.
With Task Killers I have had no problems with Rhythm Task Manager but couldn't seem to figure out how to set a few others so they wouldn't cause issues with my phone. One issue was a couple of the Task Killers seemed to think (or something) the Fascinate was "timing out" when the screen went black when I held the phone to my ear for a phone call so one or two of them would just freeze up the phone. The Fascinate just seems like SUCH a different operating system then the rest of the Droids but I like it so much more.
If I look at my "Ignore List" I have, Phone, Calendar, Messaging, Daily Briefing, Clock, the Maize Clock Widget, Browser and Battery Status all ignored. One important setting with Rhythm seems to be making sure "Auto Kill Ignored Tasks" is unchecked as well. But Rhythm seems to work great. I haven't had my phone plugged in since 8am and am still at 76%.
The only thing I don't get is the built in app "Daily Briefing" REALLY seems to control a lot of things even though I don't even use it. I don't have "LauncherPro" installed or anything either.
Like I said, download any of this stuff at your own risk, but the above seems to work for me.