Two thoughts – are you capturing to the internal drive or a firewire drive?

Here are my thoughts:
1) you’re right. FCP has to recompess on the fly and you’re running out of time as it caches video in it’s memory, recompresses to PJPEG and writes the files. A standard DV stream could possibly work as it has no additional compression.

2) You could capture DV and then recompress to PJPEG after you capture.

3) There may be a data collision occurring – This is why you ought to have two Firewire connections each on it’s own bus. One on the CPU, a second as a PCMCIA card.

You know how to get in contact if you have other questions.