This is a quote from the manual.
- Time codes are not recorded on Motion Pictures recorded when the [Rec Format] is set to [MP4].
I didn't realize this either but it makes sense now. I came across this post researching why the time code doesn't match when recording mov files. It is correct on the display when recording (matches internal clock) but Premiere Pro (cs5.5) is off by about 3 hours when using the time code effect.
Thanks Cole! Looks like there's no chance to resurrect the timecode from MP4, but from now I'll shoot on MOV only. About Premiere Pro in my case (CS6) timecode effect works fine. Thanks again for a quote from manual!