Well, my little video project is borked again. This is good experience... I guess.
Evidentally the source was somehow corrupted on the way to the raw video feed, which was just exacerrated when it was encoded & multiplexed into a composite file. Thppppttt.
Of course, I didn't find this out until I had ripped everything. Again. Oh well. Now I have to re-rip everything... and this time it wouldn't have helped at all to keep the raw files, since evidentally they're the ones at fault.
So now the plan is to try a few different ways of doing things: clean the tape head and make sure that's not the problem (I doubt it is), update libdv to see if that helps (it might), rip the video stream as AVI instead of raw DV (who knows), try using the command-line ffmpeg instead of Kino's invocation. One would hope at least one version would be verifiable by mpgtx.
Delete everything! Start again! w00t!