A slow hard drive (external FireWire drives can sometimes be slow, or using the “System Disk” on the Mac for capturing can cause problems.
You might have a corrupt capture file or two, if the problem persists after you try the following, try to recapture the “bad” clips.
There is a function in FCP that is often overlooked… and it can help with many audio and video “skipping”, “sticking” and “missing” problems.
You should “Mixdown” the Audio for playback before you dub out of FCP, or during the edit, if you have audio/video stuttering, drop-outs, sync-slippage, or freezes.
NOTE: Mixdown has even been demonstrated to help with slipping, skipping problems (or “missing” audio clips) for files being EXPORTED as QT (or similar) files out of FCP.
First, SELECT ALL of your audio tracks (highlight them) on the timeline, then:
Sequence Menu > Render Only > Mixdown.
You should see a dialog box telling you its rendering.
It might seem to make little sense that “Mixing down” even simple audio tracks will “fix” complex video “freezes” or random audio dropouts to tape or export, but it CAN.
NOTE: It does not matter of you only have one audio track, if there are random freezes during output, you should try the Mixdown.