He also admits quite readily that he dislikes going to the bathroom, but won't explain why.
Does he just dislike using the bathroom at school? If so, could it be the noise of the flush? Personally, I can't stand the sound of flushing toilets in public places - I think it's the 'industrial size' sound in the small confined stall with nothing to absorb some of the hollow, echo-y sound. I have to cover my ears when flushing public toilets and I've noticed that DS does it too.
One other thing that comes to mind, is that when DS was in a part-day pre-school, the toilet backed up once and overflowed. It scared him silly and he refused to use that bathroom for quite awhile - he was afraid it would happen again.
Just a thought...