Fan control circuit not working, Fan remains ON
To put the PNP transistor in cutoff you need to bring THERM up to the transistor's emitter voltage, 5V, instead of just 3.3V. You could connect R18 to 5V but that might damage the temperature sensor.

The general solution to this problem is to add an NPN transistor that will drive the base of Q3. The NPN transistor can be switched with the 3.3V sensor voltage but will easily control the PNP base. Of course, the sense of the alarm signal is now inverted so you probably need to change the setup of the THERM output accordingly.