did you get a burn in on your DV dubs?
always do that,
and always check your burn in against the actual TC.
both in your deck/camera
(best to check at the place that did the dubs, and if wrong, get them to do it again)
and check burn in against TC after capture.
but your basic assumption that this should work is correct.
FCP is pretty solid on something this simple,
you'll need to do some detective work yourself to really get to the bottom of this
are some tapes all out, others all in?
does the TC drift after a certain point on some tapes/captures?
what, if anything, do the "off" clips have in common?
did you have speed changes on the "off' clips?
(that could point to an FCP problem)
maybe there's some drop-frame issues?? ( which i wouldn't know about as i come from PAL land)
the truth is out there...
nick