I too am having the same problem.
I have done the checks and when I check the 5V between the middle leg on the transistor (GND) and the +5V pinout, when the software is not running, I get the 5V, but when the software is running I get approximately 2.3V across these pins.
Really would like to be able to solve this, I have bought a new fan, I have also replaced the BD679 darlington but still everything is the same.
Paul