Check everything else out, but I believe the fenders are usually different heights. The one on the road/slide side is lower to accommodate the slide. That said, it shouldn't rub the wheel (of course). I don't think Pod warranties are transferable, and yours might have expired anyway, but it sounds like a manufacturing defect that FR ought to fix, assuming it's not some other problem with the axle.
I recently had an explosive blowout on my slide-side tire going down the road. It blew the entire fender off completely and instantly. So I got a new one and put it on. Not a lot of trouble. Two times not a lot still isn't very much -- meaning taking the fender off and moving to a better position wouldn't be too hard, if that's what it comes to.
TT