Yeah that happens form time to time for me in UT99.
Uninstall the mouse, reboot, and when you re-attach it to your system. Do not install it, i.e. do not configure it with Mouseware. Just dismiss the new hardware found message. Let the standard windoze drivers handle it. Acceleration *should* be gone.
To make sure you don't get mouse accel ingame do the following:
In windows make sure mouse accel is set to none. If you have accel set to medium (the mouseware default) and the ingame mouse accel to 0 you will still get mouse acceleration.
Goto logitech.com and get the latest version of their drivers. On the download page you'll notice in the left sidebar a link to an advanced mouseware utility. Download and play with that. Make sure you change it from precision to speed for an mx500.
If you set mouse accel to 0 in mouseware 0 in ut2k4 and use the advanced utility changing from precision to speed etc then you shoudln't have any problem with mouse acceleration ingame.