Ah, this only happens in metacity. When I switch to compiz (switching from no desktop effects to normal effects), it goes away completely. Window position is remembered every time for Audacious (but not necessarily all other apps for some reason). So this is really a metacity bug, and I'm marking it as a duplicate of Bug #124315
Ah, this only happens in metacity. When I switch to compiz (switching from no desktop effects to normal effects), it goes away completely. Window position is remembered every time for Audacious (but not necessarily all other apps for some reason). So this is really a metacity bug, and I'm marking it as a duplicate of Bug #124315