I have a Mac Pro, about three years old, and just purchased a Magic Mouse - same issues with poor tracking and scrolling. After doing some Googling, I came across several posts that indiated many Mac Pro's were built with some of their Airport and Bluetooth antenna wiring mis-connected inside - it wouldn't affect Airport functionality, and but would severely degrade BT...
Here's one site with diagrams/pictures:
http://www.thelocale.org/files/howtos/mac-pro-bluetooth-howto.pdf
For me, the fix worked - Magic Mouse is tracking normally, and Airport still works (signal strength is the same). My Mac also boots faster, so there may have been other issues caused by this mis-wiring
I will say that for a time, I used the older Apple wireless keyboard and mouse, and didn't seem to have issues. But my Mac Pro was up on my desk then (closer), and perhaps the older products worked diferently.
If you are under warranty, I would have Apple do it - in my case, it took about 15 minutes, and had to remove drives three and four to get better access to the area - the fourth unconnected cable was also tucked in and somewhat buried beneath the drives (and has a plastic sleeve to protect it from touching anything, so don't look for the round metal connector as much as a translucent plastic sleeve covering the end of a black wire.
I STILL have issues where the mouse clicks don't work correctly - if I leave "One Finger - Secondary Click" deselected, every click on any surface area acts as a contextual click, not a "regular" single click. This even screws up the behavior of an older Apple wired mouse - fortunately, I have a Logitech wireless mouse which I can still use to set the secondary click back on, and I least have single control back.
Not sure I'm liking the behavior where you have to keep one finger raised when clicking to register a single click - it's natural on most two button mechanical mice to rest both fingers on each button, but click only one. Maybe this is because I'm forced to use the Secondary click mode for now - not sure...
Message was edited by: Greg Bastug1