First thing I'd like you to do is to make absolutely sure you have the latest version of EVGA Precision installed (last week's version). Then retest again. When you are on the desktop with no apps running the GPU will downclock to conserve power in 2D mode. This is normal. When you open a 3D app then clocks should come back up to normal.

I had EVGA Precision 3.0.2.   I've updated to 3.0.3 but I still have the same problem.   "Frame Rate target" is not checked.
 
I just tried running the Heaven 3.0 benchmark a few times after updaing Precision and rebooting.  The first few time I started up Heaven one of the cards would downclock to 324MHz for a few seconds periodically, but now it's running fine without any down clocking.
 

I swapped the card and GPU1 now shows the power shoot up and clock rate drop periodically under load.   I'll send the card back.
 
 

Newegg has already approved my RMA for replacement so I'm sending it back.  It's definitely a problem with the GPU.   I ran each GPU independently and one of them works flawlessly.   The other GPU has the downclocking/power issue under load which causes very low frame rates.   The problem does seem to be worse if my PC has been shutdown for a while before running a benchmark.   If I shutdown for 30 minutes, power up and start Heaven, the thing is spiking and stuttering every 10-15 seconds like clock work.    It gets better after a while but I still see spikes even after running Heaven or a game for an hour.
 
I hate to be without the card during the replacement process, but there is obviously an issue with one of my cards.
If EVGA wants to replicate the problem then they can have mine, just send me one that works :)
 
 

Glad to hear you got your issues worked out. Enjoy those suckers

WOW your card is not supposed to down clock that low in a game or benchmark like Heaven. IDK what to tell you but you might have a defective card. I would be like **** if my card did that. 

I have Logitech Profiler, Setpoint and wireless keyboard all running in the system tray.   These were not a problem for me.  Only one of the two cards that I received had this problem.   I sent it back for a replacement and now both cards work fine.

I have one gtx 680 ftw 4gb and have the exact same problem. Once every 20 to 30 seconds the card down clocks for about 4 or 5 seconds to 324 right in the middle of BF3 (from average of 120fps to 17fps) or any game or benchmark. After pc is on for about 20+ minutes or after running 1 or 2 benchmarks it runs fine until pc is restarted again. Is it drivers or should I RMA ?

Okay, I have had a chance to do some testing. I tried one card at a time in my 1st PCIE X16 Slot. Both of my cards are having the same problem. I'm going to try both of my cards in my 2nd PCIE X16 Slot which is off the nf200 chip to make sure its not a problem with the native slots. I don't think they are the problem because both native slots ran my 2 EVGA GTX 590's just fine. I'll post again later with the results.
 
 
Okay, This is my findings. Both cards are downclocking to 324MHz under load for a few about 2-3 second every about 20 second after first boot. The cards seem to run fine after my PC is running at ideal for about 30 minutes or after running them under load for about 10-15 minutes using either bench marks or gaming. I've tried each card one at a time in both PCIE x16 slot #1 (which Native) and #2 (which is off the NF200 chip). I'm having the same problem with both. I've tried uninstalling and reinstalling the drivers and I always only install the Graphics driver and Physx. After uninstalling the drivers I reboot so the VGA pickups then I reboot again into safe mode and use driver sweeper. Then I reboot into normal mode and install the driver and always do a clean install. I'm also pretty sure its not a problem with the PSU because as I stated before my 2 GTX590's ran just fine.
 
I'm not sure if I have the worst luck in the world or if there is something else wrong that I should check. But with everything I have done it seems to me both of my cards are bad. This really makes me rethink my decision of buy EVGA next time.

Tried next 2 drivers still downclocking time for RMA