If you turn off the camera between takes it can soemtimes break.
If you review your previous take and don't re-sync the timecode.
If you play or fast-forward on the tape so there's a section with no recording.
To fix: press Rec Check on top of camera. It will run camera to end of last take and Regen the tiemcode to match.
FWIW, I also noticed that Final Cut Pro HD reported timecode breaks when I tried to capture DV to an external FireWire drive over the same bus. The solution here is to capture to another drive.