Hi @Maciek
Thank you for your interest in the NXP MIMXRT product, I would like to provide service for you.
It's better to share some code snap about your issues, eg, which code will caused the issues, then which code will not.
You mentioned call to GPIO_PortToggle() inside the ISR for PIT timer will meet issues, please tell us which GPIO you are controlling? SWD related interface or the BOOT_MOD related pins?
Do you try to control the led pins, whether that still have issues.
From your description, your issue mainly related to your own project, can you add some code on the SDK PIT? Whether that SDK project will meet issues or not, the GPIO just use the on board LED pin.
Any updated information, kindly let me know.
Best Regards,
kerry