I just fell upon your posts because I am having the same problem. I was wondering what deck everyone is using? It sounds like this might be a compatibility issue with a certain deck. I am also capturing mini-dv footage using a Sony HDV deck. The model is HVR-M15U and I am running final cut pro 6.0.1. If this is a deck issue, Sony and Apple should get together to find a patch for it. I was already successful with a similar issue with a JVC deck that was “supported” by apple for use with FCP but having compatibility problems and creating imaginary timecode breaks. In the end JVC and apple worked together to create a software upgrade that fixed the problem.
If you are using the same deck, please let me know. If it is a deck issue hopefully we can get a fix that will improve our post efficiency.
Thanks.
Arielle