Actually, after thinking about it, I have seen a type of foam production with skimmers in FW. Those systems used moderate to large amounts of slime promoters/regenerators (eg: Novaqua) and meds such as melafix/pimafix. The aloes and oils in these products will cause foam production in FW tanks using skimmers. The same can occur in tanks fed large amounts of FD plankton/krill.
But, on a regular FW setup with a moderate bio-load, a protein skimmer shouldn't work unless there are dangerous levels of proteins, fats, urea, and ketones. If the tank has an odor, boost the water change routine.