I am not 100% certain, what the new patch did, but it something to eyefinity and 3 monitor setups.
On my HD7990 I've been running a 3 screen Eyefinity setup for 6 months using 3 identical mini DP active adapters and after the patch only 2 screens can managed through CCC.
CCC can see the 3rd monitor fine, it is just disabled. And it cannot be activated by any means.
I solved my issue by using a different mini DP adapter and suddenly I could use all 3 screens again. But that meant a return of the screen tearing that happens when you use different types of adapters. So for now I am happy to have 3 screens working again, but it is by no means a good fix, cause the screen tearing is horrible compared to before.
Setting up Eyefinity and the replacing the adapter with the old working one automatically removes the 3rd display from the eyefinity group.
My guess is that the new drivers (and 13.12 as well, tested that as well) look to the frequencies in each adapter to differentiate each screen, but if you have several identical adapters, it cannot differentiate between them and only use the standard 2 screens which can almost always be detected. Kinda dodgy description, so bear with me
It is solely an Eyefinity issue. But the problem persists after reformat/reinstall, so it must be driver related and something that worked pre 13.12 was removed in the subsequent drivers.