Hello,
Please help me to clarify if I understand this issue correctly.
Could you possibly specify which board are you using? (DevKit / EVB / Custom board)
Does the problem occurs if you debug a single SDK project?
Can you try to create a new SDK project from example e.g. "pit_periodic_interrupt_mpc5744p"
generate the code, build and debug. Are you able to pass mode transition in this project?
Now if you are jumping from one project to the other - does it mean you have a bootloader and application?
So the bootloader project pass the clock init whereas the application which you jump into does not pass the clock initialization?
This will help us to resolve this issue much faster.
Regards,
Stan