Hi Peter,
We checked all the below possibilities.
1. Confirmed the connected pin for measurement is PTD14.

2. Analyzer was set to highest available sample rate and also tried with the scope. In both cases, the result is same.

3. Tried with lower CLKOUT_RUN frequency and enabling the drive strength as well, still the same result.
4. Tried with both PTB5 & PTD14 which can be configured as CLKOUT_RUN and the result is same in all the pins. Couldn't test PTD10 since there is no GPIO tap out available to test it.

Note: PTD14 & PTB5 - GPIO Standard Plus (Switching up to 50 MHz and the CLKOUT_RUN is configured as 20MHz), PTD10 - GPIO Fast (Switching up to 120 MHz). Also as per the requirement, we have used PTD14 as the CLKOUT_RUN mode.
We have an LED blinking code and it is working as per the timings we have configured it to toggle. Basically what I have observed till now is, the expected clock frequency is generated but the same is not reflecting in the PTD14 pin whose GPIO mode is configured as CLKOUT_RUN.
Is there any other configuration which should be done other the above configurations? Can you please try to simulate and verify on S32K388 EVB just to make sure it is not the issue of the EVB?
This is the blocker point for us right now.
Regards,
Punith Chandra.