OK, installed Crysis 3, all was fine for the first 5 minutes running at 70+FPS (everything set to Very High), then I got the same drop, down to 10FPS, and Afterburner shows the same drop on both GPU1 and GPU2 usage.
OK so now we've ruled out it being a game issue, and for now, it's looking like it's definitely system related.
I've been thinking. I play BL2 a lot, and one of the things about BL2, is that it's horribly CPU bound. It being CPU bound is a result of it being both a DX9 title, and not being very well coded.
Even with a 3930K overclocked to 4.5ghz, I still experience frame rate drops every now and then with PhysX enabled, as PhysX increases the amount of draw calls due to the extra particle effects.
Anyway, the frame rate drops I get in BL2 are similar to what you're experiencing. Basically, it lasts for a few seconds, then corrects itself. When I look at the MSI Afterburner output, I see decreases in GPU usage during the drop outs..
So what I'm thinking, is that you could be CPU bottlenecked. The 8350 is a robust CPU, but it's nowhere near as good as a Core i7 in IPC, and especially for feeding SLI'd GPUs.
So here's what I recommend to test if you are CPU bottlenecked. Overclock your CPU as high as it will go whilst remaining stable. Those CPUs are admirable overclockers from what I hear, although I've never tried it personally as I only run Intel. You should be able to hit at least 4.5ghz.
If you are CPU bottlenecked, then increasing the CPU speed will definitely mitigate the drop outs, if not eliminate them completely.
And since you are running on Windows 7, it would compound the issue. Windows 8/8.1 has a much more intelligent thread scheduler, which uses the CPU more effectively than Windows 7. For a low IPC multicore processor like the 8350, using Windows 8/8.1 would help a lot I would think in CPU bound situations.