Hi, @Patrick_K,
Thank you for using MBDT for i.MX on your projects.
I have downloaded the attached example and tried to run it on my side considering your specific requirements of using the GPT2 instance with two channels configured but I didn't encounter any issues.
I have replaced the two subsystems provided with an LED toggle, but I have kept the logic for the interrupts generated by the GPT2 peripheral. The attached example demonstrates how the board LED is controlled by two interrupts from channel 1 and channel 2. The interrupt from channel 2 occurs every 2 seconds and turns on the LED, while the interrupt from channel 1 occurs every 2.5 seconds and turns off the LED right after it has been on for 0.5 seconds.
In the picture below is the actual configuration, where I highlighted the Output Compare interrupt enablement for both Channel 1 and Channel 2, along with the Compare value (period) that is set to 2 seconds for the second channel and to 2.5 seconds for the first one.

Please let me know if this model works as expected on your side and if it helps you find the issue with your project.
Cheers,
Victor