I'm not familiar with Gosign, but normally I don't see automated regmark creation where the artwork is so close to (what I assume) is the XY line. Most RIPS or plugins will leave TOO much room around marks. Maybe there's print too close to some of the marks and it's getting a false reading at certain points? Marks should have about a half inch clearance around them, although technically you can get away with things being much closer, you just need to know how and where the eye reads things.
Does the job allow you to print and cut shorter sheets?