The Victor fans should be wired to the left terminals (GND and +12V, not M-/M+ on the right hand side) on the Victor, right along with the connection to the appropiate fuse block.
This way, the fan operates whenever the Victor is powered. There's really no need to wire all the fans together and power them through a breaker or something (which sounds like what you did); it sounds like a good way to smoke your Victors if that circuit disconnects for some freak reason too
The fans should have absoultely no effect on robot operation in terms of driving, motor movement, etc. They only keep the Victors from overheating. If your robot is having control problems, I would suspect that there is faulty wiring elsewhere, bad code, or possibly radio interference. Can you post more details on the nature of the robot's behavior when it's spazzing out??
EDIT: A diagram of the correct wiring is on the first page of the
Innovation First User's Manual for the Victor 884.