I have a scythe fan controller. my 3 case fans are plugged into it and everything is working (i.e. knob is controlling speed, and the RPMS are being displayed). I also just added a PCI slot fan. That fan has a 4 pin molex connector. I have an adapter plugged into it. The fan controller is now controlling speed, but the RPMS aren't being displayed.
Look at the wires from the fan to the 4-pin Molex connector. A typical Molex connection system to provide power to a fan has only two wires - black (Ground) and red (+12 vdc, but in your case less than that because it is being fed by the controller). It probably has NO third lead there. On 3-pin fans you will see that there is a third wire (yellow) from fan to connector. This carries a pulse signal (generated within the fan) back to the controller to provide the fan's speed signal. I suspect the PCI slot fan has no such signal output, so he controller has no way of knowing the fan's speed.