Hi,
the mask set of the32 and 48 pin device is the same so vssx2 has no influence on output function of the pin.

Vddx = 3.3V

What is connected to the pin? Have you checked the schematic design?
Have you checked the SW for pin setup?
Where the ctm measures the pin? It can be routed to PJ0 in the case the MODRR1_PWM5RR is set to 1.
Do they measure it at correct pin? (also happened)
Could you please check PWM function at the pin whether it is working? It is also output function and if it does not generates signal then the pin is damaged.
Best regards,
Ladislav