I have that problem with my RG when i put a PAF Pro in the bridge, and now the bridge and middle together sound really weird and weak.
Personally i really like it.. in this position anyway, becasue on the
lower strings i get a really cool funky clunk kind of sound (but the high notes sound like a bee in a jamjar)
I think its phase cancellation. And if it is, simply turning the pickup around should fix it.