We are using FREE RTOS for our automotive embedded project. Scheduler based on RTOS (RTI) works fine (Functions set in periodic task i.e 5mS,10mS works fine). But when any external interrupt occurs like CAN, Frequency signals scheduler disables permanently. But interrupt routines continue to work. I couldn't figure out this issue.
The best I can do is make a wild guess, which is a waste of our time and yours, as you don't even mention which port you are using.