What kind of audio drop outs are you getting? Are you coming in embedded or AES/EBU? Are you just hearing them during capture or are they in the QT file after capture?
As for the timecode breaks, it seems to be a problem. I just finished four long 720p60 videos and I was getting so sick of the timecode breaks, I turned off the warning in FCP preferences. SOme people might find this unorthodox, but you can tell FCP to warn you of timecode breaks after capture (and not to make a new clip), and it seemed to work great for me. If this is too risky for you, simply hit escape when FCP is ‘searching for timecode break’ and then continue to capture. Most likely it will try and recapture the clip that supposedly had the timecode break without incident. I just reread that you are in FCP 5, I was using FCP 4.5. I hope there is still a preference to turn off the timecode break warnings.
Hope this helps.
Jeremy
———–
G5 Dual 2Ghz <> 4GB RAM <> FCP 4.5 <> Kona 2
ATTO 42XS <> Huge Systems 1.25 TB 4105 Fibre