One of the things that has been reinforced for me from this episode is that the USB ecosystem is remarkably shoddy. I'm still not even exactly sure where the bug was, or which two components didn't interoperate, or why. The problematic enclosure, attached to a different machine, seems to behave fine (I'm currently doing a Time Machine backup to an AppleRAID set up on the same disks and enclosure, which has been quite happy up to 231G so far).
(Edit: although the initial backup succeeded, it appears that periodic disconnects are, in fact, still an issue even on the Mac. Looks like the enclosure may be to blame after all.)