I've reassembled the stock cooler completely only to find the same issue. I guess something have completely altered the GPU by installing the hybrid kit.
I'm kinda concerned about getting a RMA because small bits of plastic got chipped off from the socket for LED control(although LED works well) during installation.
My local service center allows replacement to a new product within few weeks for initial defects of a product. I don't know if this will work or not but I still have to give it a try.