No Sahil, i am not ruling out anything. it could be the bios , m/b pci-e slot pins, etc.. or as funky rightly pointed out the TIM must have shorted some traces , chip pins on the card. but you see sahil i do not know the technical ability of the poster hence I cannot straight way ask him to undress the card and clean the card pcb with acetone, water etc.
we need to go from basic solutions to advance ones in such cases.
The problem imho is , as i have stated above, that the bios is failing to initialise the pci-e bus as it is not getting a proper reply back from the card during the initial "hand-shaking" on powerup. hence the m/b bios is defaulting to the lowest speed of x1 on the pci-e bus.
The m/b h/w is not faulty because with other cards it is working perfectly.
if sc_11 manages to remove the h/s and clean the pcb with acetone + cotton swabs properly then we can rule out shorted traces or shorted chip pins. (very high chance of rectifying this problem). now all we can do is wait for feedback from sc_11.