Try each card by itself, starting with the low hashrate one. Leave it in the current PCI-E slot and see if it gets a low hash rate by itself. If it still does, move it to the slot the normal hashrate card was in and try again. If hashrate is still low, it could be that the card is going bad? Not sure. I would try stock clocks first and see if there's any improvement.
If it improves by itself in the same slot then its probably an I/O issue with the motherboard, I would try increasing voltages (small increments!) in the BIOS for North Bridge, I/O related chipsets, and PCI-E. Depends on your board and chipset what you should adjust though.
If the card improves after moving it to the other slot, then it could be that slot it was in is having issues, try another if available.
Hope this helps.
If it improves by itself in the same slot then its probably an I/O issue with the motherboard, I would try increasing voltages (small increments!) in the BIOS for North Bridge, I/O related chipsets, and PCI-E. Depends on your board and chipset what you should adjust though.
If the card improves after moving it to the other slot, then it could be that slot it was in is having issues, try another if available.
Hope this helps.
I think the OP mentioned that the hash rate is fine.
I notice something similar with the OP - even at the same hash rates I have a GPU solving more shares than the other one, I assume it has to do with the way the mining software allocates them across GPUs.
OP - try switching the cards between them in their slots - make GPU 0 - GPU 1, and the other way around. See if the difference persists.