Our house has experienced this problem continually; and though we haven’t found a fix-all, we found an explanation.
We’re working in FCP HD on dual-deuce G5’s, too; capturing from the Sony Betacam UVW-1800, a variety of DV/S-VHS players, etc, correctly engineered in a rack. Sometimes upon Capture, notification pops up that “You’re running out of hard disk space”; once you’ve finished capturing the selection you desire and attempt to exit the Capture tool, FCP crashes with the ever-coveted Mac Spinning Wheel Of Death.
A glitch, apparently, does not get corrected when the Capture tool measures how much space is in your Capture Scratch folder. Once it assesses how much space is available, it automatically makes a file for that entire file size. Once caught in the clutches of the Spinning Wheel of Death, you wind up having to Force Quit FCP and your capture is, most often if not always, obliterated.
As was recommended before, trash your Prefs, restart, and— most often, just the act of engaging the Capture tool again is enough to set it correct.