The only difference between PCIe 1x and PCIe 16x is bandwidth, and mining requires very little. Some of the FPGA miners I've read about use simple serial links for getwork calls, and that's significantly less available bandwidth than a PCIe 1x slot on the mobo.
I'd look for other differences between the cards - make sure GPUz is showing the proper shader counts, gpu/mem speeds are equal, and that you're using the same miner flags.
Power issues wouldn't usually show themselves as reduced hashrates - likelier you'd see the card not responding at all in that case. Or in a dual-GPU card, maybe one of the GPUs would be inactive, effectively halving your hashrate.
Another good test would be to swap that card into the mobo and move another out to the extender; if you still get the same 140mhash directly connected, and everything else is equal, something is up with your card.
I switched out the card outside the case with one that was inside. The new out-of the-case card performed much slower than the old one, while the old one performed at the full 180 MHash/s rate while inside the case. This problem doesn't show up right away. All three cards start at a full 180 MHash/s, and then the card outside the case slows down. Could this be caused by overheating? There was a burning plastic smell this time.