Hello, Michael.
I am sorry you are having problems with your A-Star 32U4. It is not clear how you are setting the frequency for your PWM signal. Could you post the code you are using to set the PWM frequency? Could you also post screen captures of your oscilloscope?
By the way, the AVR on the A-Star 32U4 Prime LV does not operate at 3.3V. It operates at 5V and uses a 16Mhz crystal.
- Jeremy