I may be encountering the same issue, also on Crosshair VIII Extreme, but it probably hits other hardware too. It certainly seems to be a software issue, with frame rates taking a big hit sometimes if AC has been running. I have a suspicion that it's possibly something to do with Aura lighting that's doing it. I've noticed that the "LightingService (32 bit)" and a "WMI Provider Host" tend to be chewing a bit of CPU (viewed in Task Manager) every time I've encountered it. It's not that noticeable in terms of CPU% on a 5950X because there are so many cores/threads, but they solidly top the chart when the system is being weird and is otherwise idle. I've been playing with restarting the LightingService when it happens, trying to see if that clears the problem. Just closing AC after it has been open doesn't seem to properly clear the problem, but I think restarting that service may help. Restarting NT services randomly isn't something I'd encourage, and can cause problems, so this is a very specific thing to this problem.
1. Win+R, services.msc
2. Scroll down to LightingService
3. Right click LightingService, select Restart
4. Aura will kinda break (animations stop, lights may drop out for a second), but then seems to recover
Resist the temptation to mess with services as a whole, unless you understand what they do. You can very easily break NT systems by disabling or restarting the wrong service. Very much at your own risk, but restarting LightingService seems to be safe enough.
I'm not 100% that actually solves the issue, or that the problem is actually in LightingService. One of possibilities is that the problem is in something else which talks to LightingService, and restarting that causes the other thing to stop misbehaving. For reference, I have been running with everything enabled for Aura Sync, and have been typically running in Rainbow mode and high Aura CPU usage enabled. The lighting runs just fine like that after a reboot, with other things behaving normally; it's only after running AC that something seems to get into a bad state.
The above are preliminary observations, I've only been properly investigating it for a couple of days.