Have you tested more than one software?
How many motherboards do you have affected? If just one, It also could be that the output header is defective as well.
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Thanks for the response. I have tried with Microsoft cirtest.exe from the Windows Device Driver SDK and with Windows Media Center installed under 32 bit Windows 7. Neither seems to generate an IR output. The behaviour is the same on both of the IR output header ports so unless the whole CIR chip has failed there is probably not a hardware fault. I only have one DZ68DB work which has been installed from new in a PC chassis under workshop anti-static conditions.
It would be very helpful to get confirmation that the CIR output is actually supported and operational under Windows 7 on this type of motherboard before I look at replacing the board under warranty.