Hi
This will be my first post as well then
I doubt it would be a firmware problem. I've compiled my own from stock Marlin without any problems, so a custom TH3D firmware specific for this printer should be tested and fine.
Are you sure it worked before the upgrade? And better yet, is your part cooling fan working??
If you just turned it on after the upgrade and started to check things and suddenly noticed the control box fan isn't working you should know this:
The control box fan is connected on the same controller output as the part cooling fan on the Ender-3 (at least it was on my version), when you just turn your printer on the fan is off ...
And if you don't have the part cooling fan on (during printing) your electronics can get a bit hot
I simply rewired my control box fan, so now it is always on when the printer is on.