I sincerely apologize if I am stating the obvious, but just in case you haven't double checked yet, make sure the fan speed sense wire is connected to your "CPU Fan" connector on your motherboard. Just in case you don't know already, you can connect your CPU fan directly to a power supply connector if you want to, just as long as the third fan-speed Sense wire is connected to the CPU fan connector. Without this connection, the motherboard will refuse to boot, thinking the CPU fan is not working. This is a safety feature to protect your CPU from burning up, which it would do pretty quickly if the fan really was not working. Sorry if I am stating the obvious.