Hello Stephane,
My understanding is that the PWM output is derived from the TPM module, and the GPIO driver becomes disconnected when the TPM mode is enabled. It is also possible that the maximum allowable TPM output current is different than the combined output current limit for all pins of 100mA
Perhaps you might check whether you get similar results with the other TPM channels and/or a replacement device. It is possible that the particular device is damaged, and you will need to rule this out.
If you are attempting to directly drive a high power FET, keep in mind that the gate input capacitance can be quite large. You need to include a series resistor to limit the output current to a safe value for the MCU. If the presence of such a resistor results in slow rise time at the FET gate, when compared with the PWM period, this would indicate that an additional high current driver is necessary ot overcome the effects of the gate capacitance. For 3.3 volt operation, I might suggest a current limiting resistor of say, 330 ohms.
Regards,
Mac