I bought a barebones kit, and the heatsink fan included in the package came with a plug that has three pins while the CPU fan connector has four pins. Next to it is the chassis fan connector and it has three pins. I connected my cpu fan to it. It is running well. Will that be a problem?
On a three-pin fan, the pins are for (1) ground, (2) 12v and (3) speed indication (in BIOS or Windows). The 4th pin allows speed control or PWM (pulse-width modulation, a means of controlling speed on DC motors). If you connect a 3-pin fan to a header that's not labelled for your CPU, you'll be fine as it'll just spin, although if BIOS isn't detecting CPU fan speed (with your fan connected to the chassis fan header) I'm surprised it's not throwing up an alert. Guess that depends upon the BIOS / mobo manufacturer.
Thanks for all the replies. I found them very helpful. I was able to plug the CPU fan into the four pin connector because the slot is off-centered to allow for it. I hadn't noticed that before. This particular mobo has a program that lets you monitor the speed and temp of the cpu and mobo from windows, which is nice.