The fan on my card is clearly running but there is no reading in CCC or GPU-Z for the speed (it's just 0%).
I was encountering the horrible screech/click/bike pedal sound so I tried a couple of restarts and it went away. Between restarts the percent just disappeared. It was set at 60, now it's 0. I dismantled the card and applied some WD-40 to the fan. No more sound, but still no fan speed reading.
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.
I went into gpu-z just to check mine...it says I'm going at 40%. It's not set to show minimum instead of current? It sounds like your fan is working fine you just don't have a way to prove it anymore...you might also check to see if there is a bios option for the PCIe slot fan.