For that to happen someone must have let oil get under the F/E iron and soak into the wood around the screws. You might try drilling out the nut holes slightly to see if you can get into good, clean wood, then try the Acraglass again, marring the walls of the holes a bit to give the Acraglass a better hold.
If that doesn't work, I'd prolly try to find a replacement F/E at a good price.
If that didn't work out, I'd probably remove the inset nuts, drill a 1/2" hole around the existing holes, epoxy in a piece of dense walnut dowell (might have to make it) and sand and stain, then drill the screw holes and inset holes and reset the nuts, then refinish and rechecker.
Another option would be to make larger inset nuts, assuming you could find a threading die to match the existing screws, or go to new, larger nuts and new, larger screws. While the dowells sound like a good bit of work, I think they'd be less than making new nuts etc. and prolly look better.
Good luck, these are great, old guns that are certainly worth the effort.