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Higher frame rate means higher load on the GPU. Higher load means more power draw and higher temperature. Both of those can cause the card to reduce the clock speed.
What are your GPU temperatures when this happens? What's your power limit set to? What's your target temperature set to?
Indeed, I have it running with V-Sync off on both 60Hz settings and 144Hz.
GPU temperatures vary depending on game. But GPU 1 usually never surpasses 82 degrees C, GPU 2 doesn't surpass 70 degrees C - Doubt it's throttling.
I set the power limit to +20% before and it had no effect.
Also this happens instantaneously, even with the cards @ lower temps the GPU clock fluctuates as soon as I boot up a game.
Ah so I think I've narrowed it down to a fullscreen problem. It worked perfectly until I alt-tabbed out and then back in. Then it started downclocking again in Far Cry 4.
Never had this problem before. It sometimes works but for the majority it downclocks or hovers around 950-1000MHz. Also I noticed a slight flicker of the windows bar while in fullscreen. I'm really not sure what's going on here...
Answer: Overlooked the fact that my second PCI-E bus was only rated for x4. Meaning I was running in 16x and 4x - The clocks adjusted accordingly
Disabling Crossfire and running 3D Mark confirmed this
Not even disappointed, problem has been routed (as nicely pointed out by a user on Hardware Canucks.)
Solution: Getting a new MOBO