I would start with what smoke suggested. If it's the print and cut alignment, basically there are 2 different alignments, and they have slightly different names in the control panel when you are punching in the calibration values. I think one is called PC cut, and the other name I am forgetting.
- 1 - is the alignment when crop marks are printed on the output
- 2 - is the alignment when we cut a print without scanning any alignment marks. This only works directly after a print has been made followed by cutting. It can still position fairly accurately, but in my experience is not quite the precision you get with the version using alignment marks. For me there have been a few media that the marks are hard to read on, so I've had to occasionally use the version without marks with decent success. Having the marks is preferred if you are able to print them.