In an attempt to isolate the problem, have you tried other negatives?
Going another direction, the following older thread that I just happened to read recently on the LF Forum, is pretty critical of the contact frames from Photographer's Formulary. There are complaints having to do with uneven pressure which does seem to be the problem you describe.
I have no personal experience with Photographer's Formulary frames. I have 8x10 and 11x14 sizes from Bostick & Sullivan and 7x17 made by Bill Schwab. After Photostock you have to wonder when he had time to make contact frames, but it works perfectly.