Well I still have yet to have these problems since hard resesting and turning off device after ... while plugged in and unchecking the today timeout (er crap, maybe I did have it happen once?).
I am planning on taking my phone in this week to hopefully get it replaced, but its going to be very hard to ever rely on it now... I will probably forever have to set an alarm clock in addition to my phone, until/unless they release an update that specifically states it fixes this problem...