Could it be stains from retained developer, not neutralised in the stop bath, reacting with the fixer? If so, you might need to a) use a stronger stop bath b) make sure your stop bath is fresh c) increase the time the print spends in the stop bath d) drain the print of developer before putting into the stop bath.
Alternatively, you could be picking up chemical contamination on the backs of the prints from somewhere. I think selenium toner leaves pink stains IIRC.
If you're drying prints flat on screens or otherwise, water can accumulate in dips and cause staining as it dries. Perhaps moisture is remaining trapped behind the prints as they dry face-up and marking the back. Some older-style papers are really vulnerable to these problems; I had tons of fun with water pools on dead matt Multigrade IVFB; it took me ages to work out why it was staining - that was on the emulsion but it's possible the same thing is happening to your prints.
Just a few suggestions, and probably miles out. :-D