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Does the transistor get hot?

How did you measure Ib?

You need to use a 'scope with either a current probe or to measure the voltage across R3 and working out the current using Ohm's law. If you use a meter, you can only accurately measure it when the duty cycle is 100% because the  meter will only accurately measure DC or 50/60Hz AC.

Here's another idea using a PNP transistor to switch the positive side of the fan's power supply.

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How do did you calculate it?

I reckon IB wil be between 17mA and 21mA, my calculations are shown below:

IB(Q1) = (VDD -  VBE(Q2) - VBE(Q1))/R3

With VBE = 0.7V

IB = (3.3 - 0.7 - 0.7)/100 = 0.019 = 19mA

If VBE is lower IB will be higher and vice versa.

I didn't account for R4 because the current though it will be tiny, 0.6/1000 so won't effect the calculation.

Do you think I've gone wrong somewhere?

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What do you mean by Roth?

I'm glad you got it working but give 68R in the parts list as 67R will be hard if not impossible to get hold of because it's not a standard value.

I don't see why it should limit the minimum duty cycle though, the transistors should be able to turn off continuously, enabling a duty cycle of zero.

Does the fan draw a hight peak current when the duty cycle is low? You'd need a 'scope to measure it but that would make sense.

What transistors are you using?

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