Using mod_xinerama patch and dual screen setup will lead to opening _some_ floating windows at position sth near to half of whlie xinerama width instead of screen width. I think that happens only to applications which explicitely ask for beeing placed in the middle of screen.
Any specific apps that seem prone to this behavior?
Priority reduced to '3' until this can be reproduced
Using Oracle's java: "javaws /dev/null" will reproduce this.