Well, naturally, not a day goes by and I find something to complain about...
Xvid seems to die when I try to use it, the video doesn't start playing. Any other codec I try (Alpary lossless, Huffyuv, uncompressed AVI) seems to not only drop frames (I get 130 out of 151 at best), but also to create frames like this, amalgamated from two separate frames:
And not only at scene changes.
I tried turning off hardware acceleration and changing the color quality of the display, since Hypercam seems to say those things can help, but no go.