PaulS:
Appearently, you need more equipment to process the PWM signal. I don't know.
Clearly. Since you posted no wiring diagram to show how you connected the transistor, all we can do is assume that you didn't connect it properly.
The PWM pin has no idea what it connected to it. It turns the pin on and off at the appropriate times, with the appropriate duty cycle, regardless of what is connected to it - LED, transistor, rutabaga, or nothing.
Sorry. I didn't know there were multiple ways to connect a transistor.
The transistor is between the negative lead of the fan. The center pin of the transistor is connect to pin 18 of the pi. There is a capacitor between the fans + & - lead, for it to have enough power to kick on and not draw to much from the device.
The fan won't kick on with 3.3v. Which is the rating I get with my multimeter from the PWM signal set at 1023. It will with direct 5v.