I have this exact problem with the Samsung Galaxy S... The clock stops updating overnight, when the phone goes to sleep, so my alarm never goes off
Then it updates after a couple seconds when you turn the screen back on.
I don't use a task killer. Nor do i have a paused audiobook. And my phone is on airplane mode overnight so there are no email notifications. I think the problem is somewhat deeper, and android related, not phone-specific =\
If anybody can find a fix for this i will love you forever (figuratively).