Same issue here. I have had issues with this software since I purchased my case, it's complete garbage and they can't seem to fix it. Half of the time the TTRGB software just stops running, disappears from my tray - and I have to manually start it again just to get the colors working again. And yes, with the issue you are reporting you can't use PWM - so we have to manually set our fans to a constant RPM.
I would never recommend TT's fans / controllers to anyone. If you even look at this forum their products are so riddled with bugs it's ludicrous. And they can't seem to fix any of them.
If I didn't have to remove my GPU (watercooled) to access my Aura headers I'd already have swapped out this #### program for something else. Next time I clear my loop it will be gone.