The fan is connected to the card via a 2 pin. The only connection to the motherboard is through the PCIe slot. Everything is how it was before on the card itself as far as I can tell. I just took another look at it and still don't see why-oh-why this is happening.
Temps and clock speeds are still able to be altered. Both changes appear in GPU-Z and CCC. I'm keeping it at stock for now though, I sense fan speed would be helpful in a true OC.