Mike, all I can suggest is to make sure you’re using a really clean and good VCR (an SVHS machine may be even better) as it sounds like you might have tracking issues which will mess up a capture.
The other thing is to make sure the tape has been rolling for at least 5 sec. before you hit the capture button.
If none of the above work (and you have some extra money lying around), invest in an ADVC300 as it has a built-in TBC which will help correct errors.
Good luck with the project.