I have a Asrock Z77E ITX motherboard. I've had it since September but waited for gpu prices to drop down meaning I was running the on board gpu for sometime.

I bought a 7970 and had issues with the motherboard recognizing it since the beginning. Somehow after updating bios I was able to get it to work (took it out a couple of times, tried the cables etc.)
After I finally got it to work it ran fine.

Yesterday I installed a new cooler for the GPU but know I have the same annoying issue. Bios won't recognize the card (says PCI-E is empty) which is exactly as before. However, now I can't seem to get it to work.
I have read one post similar to this but the helps on that one didn't work (reset cmos, update bios, take the card out...). Power source is fine and I am able to use the computer while typing this using on board gpu. The external just doesn't seem to work.

Any ideas what I should try next? Using the motherboard as a target for shooting is also an option...