You only put in the stand-offs that the mobo uses, no more and no less.
So unless your case is crooked it should fit perfectly... so might wanna look into that properly.
As far as your issue goes ... that mobo is equipped with a Back-up BIOS.
Try following the procedure on this page to force the Back-up BIOS being flashed back to the main BIOS chip.
DO NOT TOUCH THAT POWER BUTTON, LET IT DO IT ITSELF.
http://forum.giga-byte.co.uk/index.php?topic=9462.0
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Having said this ... this pertains as to a post from 2012... since I cannot easily find how to trigger the b_bios on the Gaming 3 so it copies it back.
Check your manual on this or perhaps there's a switch on the Mobo itself.
If it's a simple BIOS fault .. forcing the Back-Up BIOS to kick in may fix your issue.
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Edit:
GigaByte tends to respond quickly and fast to Tech Support questions by people not retarded.
So if you can't find the official way of doing it you should shoot over a mail to them asking them how to force it.
Note: When you do this do so from a different mail account than your primary one you'd use for RMA procedures, also a different name.