Are we talking about the stiffeners made out of stamped angle that is notched to show where to cut?
I can't remember if in my case it was rudder or elevators, but I had the same thing happen. Don't know if I got two "lefts" & no "rights" or something, but no matter how many times I twisted and turned things, the reality was if you cut to those pre-punched notches, you ended up with a couple of sets of stiffeners that had the flanges opposite how they were depicted on the print.
I called Vans and they said in this case it didn't matter which way the flanges faced as long as they were a matched set top/bottom so the flanges didn't interfere with each other rat the trailing edge.