From my limited post production knowledge, the problem lies between avchd and prores themselves, an issue which fcp recognizes too. I understand that they have come out with a fcp7 fix/upgrade that allows direct editing on avchd instead of prores.
The suggestions by Dixon are also truly valid.
The next time you have long recording, I hear that by NOT choosing LPCM for audio (that is if you are using Panasonic AF102, I don't know about other cameras), log and transfer can be really fast... though I have not personally tried it.