Thanks for the compliments guys, but the credit should go to Frank for noticing the system clock correlation and Marius for doing the real investigation and patch (the rest was just a few bugtracker queries, nothing to write home about).

Unfortunately that's not the end of the story: applying that patch results in both RANDR and XINERAMA extensions getting disabled :-( Anyone know how to get logs out of Xomap?

EDIT: False alarm, that was a build problem. I was using dpatch to manage patches, but it turns out the xorg-server build scaffolding is already tooled with quilt. Since the original source package doesn't contain any patches I didn't notice, and once I added a second patch it broke spectacularly (I'm surprised it ever worked in the first place).

The good news is that the bug seems fixed, rotation continues working even after setting the clock several days into the future and back.