Even though you have the second MSI 7970 disabled, try running the game with that card physically removed from the PC.
FF14 doesn't exactly fully support CrossFire (the ATI/AMD version of nVidia SLI, a multi GPU system) even though the DX11 system does, so even though the card is disabled, the DX11 system might still see it, which then causes the game to try to utilize it, which it can't, which may cause the issues.