Let me see if I understand your issue correctly. Any device connected to the second HDMI port cannot be detected; is this correct? Otherwise, kindly elaborate.
I'll try to update drivers and BIOS but honestly I don't see how this would fix the issue as it suddenly appeared after the system worked flawlessly for months with its current drivers/BIOS.
And yes, the display on the 2nd HDMI port is no longer detected. Indeed when I try to setup muti-display with the Win7 means, it doesn't detect a 2nd display and just offers me to assume a VGA connection as 2nd display instead.
Updated BIOS, graphics and chipset drivers. No change. 2nd HMDI is not working any more.
For the sake of completeness: as suddenly as this issue appeared, it also went away again. One week or so after I gave up on this and about two weeks after I first noticed it, the 2nd HDMI output was suddenly there again. Even the original "clone display" setting was there again. Apart from an automatic windows update, nothing was installed or changed.
My only guess is that one of the automatic Windows updates destroyed something and the next automatic update fixed it silently.