I had a similar problem on 4.5 and it drove me nuts. My audio didn’t completely dropout though, the levels went WAY down. I tried everything. Dumping prefs, Mixing down audio (did you try this? – might do the trick), and re importing the sound file. Nothing worked. I finally spliced in the file right where it had been dropping, so I had two separate files matched up (the second one had no keyframes or anything) and it finally worked. Don’t know if this helped or not, but I hope you got some food.
I just upgraded to FCP5 and am experiencing audio dropouts on CAPTURE and can’t figure it out. I posted a thread just now about it. Why can’t this expensive $@#^ just work the way it is supposed to – ARRGHHH!