DM,
Lsdmeasap may well be correct but only for some 4-pin fans. It could depend, I think, on the particular fan.
Yes, I've googled the issue and it seems that, in normal PWM mode, the fourth connection carries a pulsewidth modulating signal. The speed of the fan is controlled by the duty cycle of that modulating signal.
Earlier today, I completely disconnected the fan from the 3-pin setup I had and connected it instead straight into the 4-pin PWM header on the mobo. I then powered on and quickly dived into the BIOS and made sure that CPU Smart Fan Control was enabled. However, the fan still wouldn't run. It appears to be as dead as a dodo. I've e-mailed the retailer, QuietPC, to get their view. If it really is dead, I'm sure they'll send me a replacement.