It's a long shot, but what colour are the crop marks? If they're created by a plug-in (like for making rego marks for a particular cutter) then often they get created with a specific spot colour as the stroke. For whatever reason, some spot colours cause different rips to do stupid things as they often don't have a reference (ie, how would Onyx know what "Mimaki Finecut" is supposed to look like). Try just changing it to 100% K. For the print file only - if they are for a cutter the cut file will need to retain the designated spot colour that the plug-in creates.