My SLT mount does that when my power source starts running out (powertank or AA batteries) although it did that only once because I rarely align it and ask it to track an object, so it might be something else. You should check your power supply and re-flash your hand controllers firmware and motor control firmware. A guide for which can be found
here.
NOTE: The guide above is for the original Nexstar controller, if you have the Nexstar+ a guide can be found
here.
If you have Windows 8, prepare for a wrestle with CFM!
Hope this works,
-Luke