Hi,
The root cause is the Fault protection. In fact any of 4 FAULT pins can “disable” single PWM output of the submodule. The mapping is done by DISMAP register. You may see chapter “ Fault protection” within device reference manual.
So for example if there is a fault (logic one if FLVL bit is set or logic 0 if FLVL bit cleared) on FAULT0 pin and corresponding DISA0 bit is set the PWMA output of the submodule will be disabled. Similarly for other FAULTx / DISAx pairs.
Each submodule have its DISMAP register so for each PWMX/PWMA/PWMB pin the fault protection may be enabled for certain FAULT pin.
Try to clear the DISMAP register, then you will see the output signal.
Note: internal logic level may prevent PWM output to run, so you should check the FLVLx bits in such case (only if DISx is set, but no external pin is selected for FAULT circuitry, PCR[IBE] cleared).
Best Ragards,
Petr