Compare the wires first to another 3-pin connector - make sure that the wiring is the same. I have one Panaflo, and the wires are different from the normal 3-pin configuration. Red matches red, black matches black, and yellow matches blue on the Panaflo, unless of course it uses yellow too for the RPM monitor.
Also, what's the voltage and amerage rating of the fan? It's possible that the fan could draw too much power, and damage the motherboard.