FIGURED IT OUT!!!
This is a strange fix however.
Tonight I was determined to find the problem with the pci ex1 slot. I reset the bois to default and popped the card in the x1 slot, and it worked, alongside the gfx card in the main x16 slot. So, I then determined it was a setting in the bois! After trail and error I narrowed it to a chipset setting, I had disabled the 1394/IDE controller to avoid an annoying boot message. When this option is disabled, it for some reason disables the x1 slot! I originally thought it was the graphics card because I reset the bios to default in order to revert back to the on board graphics card, and stupid me thought it had to be me removing the card that made the x1 slot work.