My phone was doing that also after charging or sitting inactive for a period of time. I bumped my low clock speed to 300 and it quit doing it. It may not be what is happening on your phone but I would try that because its an easy fix.
If that doesn't fix it up I would probably reflash the rom/kernel and see if that fixes it.
Thanks.
But I've never gone under 300. I'm actually at 500 right now to see if that helps at all (which it hasn't). I assume that's a high enough minimum that I don't need to try anything higher...