I'm running a X58 Classy 3 and I've noticed the USB 3.0 ports do not work when I overlock. I've been running this overclock for awhile and it is rock solid. I just loose USB3.0 when I load my OC profile. When I go back to default clocks and voltage the USB3.0 works fine. All options in BIOS are set properly to enable 3.0. 
 
The weirdest part is the ports will still work when I am OC'd but only as 2.0. I get the "this device can perform faster" notification for most devices. Some external drives won't show up at all when the system is OC'd
 
It's not a huge deal. I just have to go back to stock clocks when I want to move a lot of external data, more of an annoyance than anything. However, it is still really odd. Anyone else have this issue?

When you OC, do you disable anything in the BIOS that might contribute to USB 3.0 not functioning?  It could even be something that doesn't even seem to be related to USB 3.  That is the only thing that I can think of.
 
I recall the X79 Dark having certain things that needed to remain enabled for other things to work...

Certainly worth a shot contacting EVGA support.  If any board mfg'r would offer (or try to offer) assistance, it would be EVGA...