I had had them turned off for a while. Turned them on last night, and the next time I played a song with actual guitar stems, realized the guitar audio was noticeably delayed from where it ought to be - not by a tremendous amount, but enough to sound and feel wrong.
Disabling the whammy effects seemed to alleviate the issue.
For the record, my settings included A/V calibration at zeroes (albeit with hardware latency compensation enabled) and audio buffer disabled. Neither turning-off the compensation nor enabling the buffer seemed to change things, however.