Last night I had to quickly run off a batch of 30 or so 8x10 fiber prints through my Nova slot processor by hand. Near the end I got sloppy/rushed or inadequate agitation (due to tending to other sheets in the process) and ended up with 2 or 3 prints with light brownish stains at portions of the paper margin. I am trying to pinpoint where in the sloppy rushed part I introduced the problem causing the brown stains.
I think this was due to un-removed developer that was still soaked in the paper when introduced to the fixer. Or inadequate agitation in the fixer?
FIxer could be getting worn out, considering it was a batch of 30. I'd mix up some fresh fixer and refix/wash before continuing, though it won't remove the brown.
It's hard to say without seeing the stains, but could it be that the walls of the slots need cleaning? I have had brown marks in the past for that reason. If the paper was left in contact with a slot wall without agitation, this might cause a problem.
I think you've diagnosed your own problem; 20 seconds is too short a time for the stop bath with FB paper and this might be causing stains to appear when the paper hits the stop bath. I'd allow at least a minute for the alkaline developer to neutralise. Otherwise I agree with Edward that its possible that your processor needs cleaning. If you want to do a rush job you'd be better off using RC paper as that's what it's designed for. FB is more suited to dish processing. Still, 3 out of 30 ain't bad...
I've encountered this problem and I don't use a stop bath. I use a 1 minute still water soak followed by another minute spray, followed by a 1 minute TF-3 or 4 fix. This is where I think I picked up the stain. It was what looked like a fingerprint smudge in the border that dried brownish. I decided it was due to handling the print at the fixing stage and made sure my fingers were wet when lifting from fix to wash. Haven't had the problem for months.
I have only found this problem occurring when I use my fingers too much in transferring prints between trays. If your hands are not clean and dry, then there is a significant risk of cross-contamination, where you put a minute amount of developer on the print after the fix, which can cause the problem. Using tongs (which I hate) has significantly reduce these types of incidents for me.