Your reports are helping, at least - I am able to reverse their tampering very quickly once I catch it.
Debating the best cure at this point - this user account has hundreds, maybe thousands of files associated with it, not all of them neatly organized, and I'm not entirely sure how to pinpoint the problem. I am debating a complete purge, replacing sites page-by-page as I verify they are clean. It would certainly clear out some dead weight. It would probably also take several days.
Thinking. Not going to start anything drastic this late at night.
ETA: Mmmm... trying something else that's easy, making the .htaccess file read-only. Maybe they'll be unable to overwrite it.