I've been using a dark background for years now. In both my Java develpment and Windows environments, I can't stand the blaring white. A lot of it has to do with the stress that a CRT used to put on my eyes. Flashing 60+ times a second causes fatigue. With the black background, things became a lot more "relaxed". I've even began creating my own "themes" by saving off just the Fonts and Colors portions of the configuration. Currently, it's kinda a 'retro warm' with yellows, oranges, and reds.
As far your particular problem, I would suggest seeing if you have any goofy mouse drivers installed. Also, the video card or video card driver is the next place I would look. The cursor is typically accelerated through the video card, so maybe you've got a dying card??
Anyway, glad to hear someone else embraces the "calm" dark working environment. Good luck with your mouse!
- Sean