is he using Flexi's own rip program, or Rolands?
I use Flexi's "rip & print" feature & I send one file, with print info & cut info in the file that I send, & I can see everything in my production manager, including the registration marks, & exact dimensions... everything.
Everything works fine for me, so I can't imagine what's going wrong, but if he uses the Flexi rip & print feature, the clues should be right there to see.