I use Dektol, stop bath, and Ilford rapid fixer mixed film-strength (4+1).
I have been considering going to 2-bath fixing and 2-bath washing, just because of this very rare problem, but I would like to identify the actual mechanism that's causing it i.e. the chemical mechanisms that could lead to the brown spots. I don't want to change my fixing regimen if it's actually developer causing it.
I do use my Dektol until it is very old and brown. I find that this improves the image tone with this paper, but could that be causing my spots issue?