I just went through this with some HDV tapes. Every time there was a start/stop on the tape (where the operator pressed record) there was a TC jump of about 15-20 frames, enough to trip up the capture process. I left the machine alone for a few hours and when I came back it had only captured about 10 minutes worth and was just shuttling back and forth, trying to locate the break and continue. I've heard that this is true of most, if not all HDV cameras -- not sure if that's right but it's damned frustrating.
Is your TC break occuring in the middle of a take or is it only at the start/stop points? If so you may need to just reset your in and out points so they're within the take and don't include the break.
JK
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SCQT! Self-contained QuickTime ? pass it on!