I am new to the BGE, but not to smoking. Are you sure of the cooking temp? Since your butts were OK I would suspect the therm. Also what were the metal top and door set at?
I cannot imagine a butt not being done at that cooking temp in that length of time. I have done 8-9 pound butts sitting right next to each other at 250-275 in a large offset and one would take 6-7 hours and the other almost 12. So it is possible for them to be ready at different times, I agree that the odds of two seperate therms being bad are slim. Have you checked them using iced and boiling water? Have you tried checking the meat for donenss by poking it, does it have trouble supporting it's weight and also seeing if the bone will pull out easily. Not sure how long it took your son to get home, but if the butt was foiled that would have helped to finsh it and it should have had a lot of moisture.

I have had temp spikes and overcooked butts before...........you can dry them out, I proved it.

Best,