The standard first attempt at "fixing" BT problems is to do a smc and pram reset (try these first). But for mac pro's, if you are using a magic mouse say, about 3 or more feet, from the mac pro, you are most likely in for some continued aggravation. That's because the BT antenna is hidden in the back of the mac pro (faraday cage) and the magic mouse BT, for lack of better words, $ucks.
Here's a thread on this subject:
Poor Bluetooth reception and jerky mouse
Basically it comes down to wiring your own external antenna in place of the internal one already there or using a BT USB dongle. I use a dongle myself on my 2010 mac pro.