Open up the back of the unit and at the top where your punch is, take some compressed air and blow out. You could be getting remnants of your plate punches caught that would cause the plate not to fully seat properly.
We had the same problem just after install. The problem was just internal punch alignment, the punches that carry the plate through the process not the installed press punches. We purchased our unit through Fuji our Service Support Tech was Robert De-Freitas, he understands exactly what needs to be done. After that we have had NO problems.
Brian
Washington State University
University Publishing, Prepress
There was a problem with the sensor on the punch that stopped the plate from traveling through which was fixed, now the same problem is back and waiting for them to come fix it.