Are your registration marks set up correctly? i.e. are they the same in Finecut for the print compared to what the cutter is looking for? (Mark size, line width, mark shape)
Sometimes, the cutter can find the marks, even though they are wrong for what its set up for, but it won't register correctly.
Also, make SURE there is no image or print in the path of the registration marks. The cutter may be sensing these as registration marks.
Hope this helps.