Hi Ian,
I had a similar issue when I had a Z68X motherboard, some years back and it was a BIOS issue. The only way that I managed to resolve it was to contact Gigabyte Tech support who sent me a tweaked BIOS to allow the PCI card to be recognised. My card was an M-Audio Delta 1010 though not a video card.
Not sure if they will still do that though as, when I had the issue, the Z68 boards were new and not regarded as old tech but you can always contact them and ask if it is possible.