Found your issue. (look below for answer)
This is your answer. The reference coolers are known for being so hot u can cook on them. If your CCC is pushed to the limit and your doing heavy rendering then whats happening is that your GPU is downclocking itself to keep from frying. Classic issue but solved by a better cooler. If you have the cash there are a ton of cool and useful mods you can do to make it better. overall the reference pcb is great but the cooler is and was the fly in the soup. As far as a Phenom II x4. It shouldn't be the issue unless your thermo paste is applyed to heavy or to light.(how old is it btw, did you OC it and if so @ what volts) If so then same idea. TOO hot it downclocks to keep temps optimal. which will slow the overall gameplay. Most people with loops who got reference just got a block and added it in on the loop and should solve some of the issues. But My money is on Heat as the issue. Check thermo pads under the cooler on the VRM, check thermo paste for spread (or reapply better paste), use After burn and please SCREEN SHOT and post. We are detectives but cant do nothing without evidence.
If it happens to be a CPU issue. Luckly your MOBO is awesome. Get a fx6300-$110, fx-8320-$160, or fx-8350-$180 on sale, In that order is Good, Better, BEST cuz you are running a custom loop. or if your rich get the 9590 (about $250-300) cuz that this is nice but hot