Well, I think I answered my own question.
"The board features two PCI-E 16x slots (will degrade to 8x for dual-GPU), three PCI-E 1x and also two legacy PCI slots, one of which will likely be wiped out if a second GPU is installed. To the right of the absolute bottom PCI-E 1x slot is the PLX chip in all its glory. This chip essentially creates a secondary PCI-E Gen 2.0 16x lane in order to provide additional bandwidth to both S-ATA and USB 3.0. This is the reason that the native PCI-E 16x is left alone." --http://techgage.com/article/asus_p7p55d-e_pro
Could this be why my first pcie-x16 stopped working and not the other? Bad controller on the mobo? I am not an expert in computers so any incite would be appreciated.