Hi,
I have checked the PE configuration, a lof items are not set. I help you set all the PE configuration, now it is okay.
You can check the PWMB signals from GPIOG0,GPIOG1,GPIOG2,GPIOG3 and GPIOE8 and GPIOE9 pins, if you have TWR-8400 board, you can test the pin4,6,21,22,23,24 of J503 connector.
I attach the project which is based on your project.
BR
Xiangjun Rong