Time of day timecode is still timecode.
How does the drop occur? Is it at a timecode break? Or more intermittent? How much can you record before the drop occurs?
Have you ruled out the tape? That is – are you able to capture other tapes?
Also – is there any other device operating on your firewire bus?
And – one more idea – are your settings correct? That is, the proper easy setup for the footage (DV-NTSC, etc.)