Was reading Moorehead's posts about box joints but the Google got confused and wouldn't let me post reply.
I had a similar problem with my home-made jig. My cast iron Delta TS has very tight miter slots but I found that if I applied side pressure to the jig (i.e. press jig in the slot, applying pressure toward the blade in a consistant manner.) it took out the slop and made the joints perfectly. Perhaps this is your solution, dunno.
Roger