I am curious if using the added Power for Crossfire through that Molex on the Mobo can give to much power to a GPU if you are not using 3 GPU's. Will it harm the GPU's?

I ask because I am on a third GPU for this mobo and the issues seems the same. My first two were HD 6970's and were in Crossfire. Now my third is a single R9 290 and it is starting to show the same issues as what happened to the first two. What is happening is that I get random Freezes of the Entire PC. Also I have seen some games not Start that are more graphic heavy like BF4, which leads me to the GPU being an issue. Then when I try to shutdown the PC it acts like it is and then gives me a Black Screen and yet the PC does not completely power off as the lights are on and all the fans keep running. Lastly it also does not boot up all the time. The power light will come on but then I just get a Black Screen and nothing like it froze on power up. It is a real pain when I do restarts/reboots. If I wait a bit between restart/reboot the PC will usually start and I can do regular things at times just no graphic heavy games will start and those darn random freezes. These are the same issues I have seen with my older HD 6970's before they completely died. The only thing I can think of that is the same is the Mobo, CPU, and RAM. I have tested my RAM and even used other RAM and get the same thing. Even tested the Mobo with another CPU and it is the same. Everything else on the PC is different. Also I do not OC my PC, especially not my GPU's. Anyways, this is why I am wondering if the Mobo is causing the issues to my GPU's as I know the GPU is the issue and I fear it will completely die soon. The Extra Power for Crossfire through that Molex is my only idea on how it could be causing this issue. I have since unplugged it and am wondering if I messed up by plugging it in, in the first place.

Any thoughts on if that could be the issue or what it might be?