Must be the newer gigabyte boards that are causing you havoc? I've been running ga-ep45-ud3p with jap caps since early 2010, with extreme overclocks, it has been running like a beast, no problems whatsoever. Best board I've ever had. Asus, piece of junk boards, since I've owned a p5n32-e sli, I'll never even look @ em ever again for their nvidia crap 680i chipset screwup. Asus newer boards have the intel chipset, even still after chucking 350 on that junk 680i board, never again, I will buy asus board.
That sounds like the same Asus board line they decided to take a crap on me as well. ;p I can certainly vouch for the ep45 and ep35's for that matter on GA. Couple hundred of them later with no issues. Super 'Jap Caps' ftw? Same for the 970 -UD3, though not so much for mining if price is a concern.
Mess, I fully agree on the not using 16x extenders. But, there are some boards that are very picky about it. Catfish had a thread back in Aug with an intel P68 board(Asus) that had a slot that absolutly would not detect a 5th card unless he used a 16x>16x cable in it.
https://bitcointalksearch.org/topic/m.466013 After reading the first review on that board,
http://www.newegg.com/Product/Product.aspx?Item=N82E16813128487 I'm not sure I'd even try to troubleshoot it. ;p Is yours the same layout x2 16x slots, x3 1x slots? It does atleast show the 16x slots are 4x if both are being used. That is likely the issue you are having with it if using 1x extenders. Either need to plug in full 16x or check that windows is properly detecting all the intel chipset compenents. Intel Inf install will solve the last one, if its even an issue.
http://www.gigabyte.com/products/product-page.aspx?pid=3800#dl Wish you weren't across the pond as I'd take that board off your hands just to play with the Intel AMT on it. Have not had a chance to screw around with that feature yet.
Well, I'm sure you probably did everything possible. It's just in my nature to try and troubleshoot those kinds of things. Its part of what I do IRL for a living. ;p
Cheers