I confirm the same issue. Every time I update GSX, although my list of disabled jetway airports remains the same as before, if I load the sim, all those disabled airports will still show doubled parking spaces, extraneous jetways, etc. I have to do the same workaround previously discussed: select at least one airport that I've previously disabled (which does in fact show up again in the left-side column despite the exclusion), remove it again (which causes it to appear twice on the right column) then click APPLY to reapply all the same exclusions.
I presume this is a bug.