my trick for clear and perforated vinyl registration marks is the same... pause the printer after the first pass of the registration marks and lay down a 2"x2" piece of scrap vinyl you normally print on. Resume print and you're set!
i've also redrawn them after the print but it seems like more of a hassle and more chance to smear. My initial solution before that, for clear, was to put a piece of masking tape (4 pieces, actually) on the backside of the clear backing (under the registration mark)... worked like a charm... until one day my cutter "ate" my masking tape and took me forever to fish it out of the roller!