Hi @jhuang1 ,
You're configuring Option B

So, PIT is running with clock: 30 MHz, INTM running with clock 60Mhz, Core clock is 120 MHz.
I tried to configurate that same with you.





Then, I have:

This is issue case:

So, please ensure that you provide enough wait time PIT interrupt before stop timer.
Best regards,
Nhi