That sounds strange. Have you contacted AJA support? They are usually very helpful in situations like this.
Yes I have contacted AJA an am awaiting a response, thanks. I just thought I'd check the forum in case other users had seen this problem.
Haven't see this here. Please let us know if you have resolved the issue and how. If you haven't lets trouble shoot further.
What seems to have solved the problem is getting the latest bios for the motherboard. The older bios for the Asus Rampage IV Extreme was quite recent, but the newest one worked.