> When I try to recapture the logged clips, I am getting timecode breaks that
> weren't there originally, and the capture is failing.
First off, what is your Capture Scratch? What's your hardware configuration? I'd be extremely careful about using Capture Now or any other flawed workaround until you've investigated the whole problem. Especially since you've already ascertained, through your initial capture, that your tape and capture device are probably OK.
Tapes don't usually "acquire" timecode breaks. "Bad data" errors, yes, but not timecode breaks, unless you record new material onto them or mix recording formats (eg. Mini-DV and DVCam on the same Mini-DV tape).