Scenario: Debian unstable/experimental, XF86 4.2, nVidia binary drivers, USB mouse at /dev/input/mice, all working.

Last week I was able to play Quake 3 Arena. This week, I cannot, because the mouse doesn't work - but only in Q3A. Start Q3A, no pointy pointy, exit Q3A, X goes "wha? it's working!" when I swear at it. Nuking ~/.q3a and starting over doesn't produce a different outcome.

Nothing in Quake's startup output or system logs (/var/log/messages, /var/log/syslog) to indicate anything.

Questions:

1. What package upgrades could cause a change in the handling of the X mouse?
2. How the hell do I start troubleshooting this?