well several things, first when you run the game you should be binding each instance of the game to a different processor. so if you run it from the command line taskset -c 0 wine eqgame.exe patchme is binding the process to processor one. if you are executing off a desktop script it probably has it in the script and you can make one for each instance. taskset -c 1 wine eqgame.exe patchme would bind to processor two and so on.
{actually nevermind the first. i just looked at the patcher and it does it for you. i run things a bit differently}
second, what graphic settings are you running the game on? on board video cards aren't great and you might want to see if lowering the settings changes your mouse response.
run glxgears from the commandline and post it here. it will give you a message like;
pparrish@arbiter:~$ glxgears
76269 frames in 5.0 seconds = 15253.739 FPS
75428 frames in 5.0 seconds = 15085.496 FPS
75479 frames in 5.0 seconds = 15095.739 FPS
75352 frames in 5.0 seconds = 15066.634 FPS
third, you can try taskset -c 0 wine -opengl eqgame.exe patchme off the command line but i dont know if that will work.
last, you may have an issue more related to ubuntu then sod. you might want to make a detailed post on the ubuntu forums about the problem you are having and ask if anyone has had a similar issue. and when i say detailed os, wine version, video card and then some detail on what the mouse is doing.
