Computer turns on but get no display when GPU is plugged in. Only works with DVI.

As the title says. My computer has been Running fine. I recently bought a new case (500r) and while I was transplanting my H80i screw holes stripped so I had to change out my CPU cooler. I have done this numerous times. But ever since I made the change My computer will start up play the start up chime but show no display. It searchers from analog and hdmi and can't find anything. BUT when I disconnect my GPU and ONLY use the DVI port it will work. I tried plugging it back in while that was working but the Nvidia control panel can't find a GPU. The cards fan spins and everything and it does not run hot. I have tried an external build and still same issue.
My conclusion would be that either the PCIe cable is screwed up or it is my GPU. But I have no idea why I would get sound and a whole start up but no display. I can even log in.
Another thing to point out is that when both DVI and GPU are plugged in. I can't get a display from either. The only way to get a display is to take the connectors out from the GPU and restart.

Edit: About the PCIe cables. I left mine when I moved so I have to purchase some more. Other wise I would of ruled out the PCIe not working.