sounds like you've got loose wires somewhere.
ctc build quality is questionable at best.
So turn it on it's side, take the base panel off and check all the cables and plugs are solid. Then check your belts are tight and nothing moves when it shouldn't.

Are you printing from the sd card or via usb ?

Also which version of makerware desktop are you using ?
Also try flashprint (select creator pro as the printer) http://www.flashforge-usa.com/support/downloads/
link is on right side of the page.