At a guess, even though you say the BOLTS are the same thread length, could the RIMS be slightly different in so much as the holes where the bolts go through being slightly less 'meaty' for want of a better word on the BBS's than your other rims?
which in turn means that the bolts sit further in, catching on something?
I know one of the Mk2 boys had a similar thing recently (binding) and it was the bolts needing cut a few mm just to sit them far enough away if I remember rightly