Have you made sure that you do not use the same registers in both interrupts or main program and interrupt without saving them inside higher priority interrupt/code? Make sure procedures do not interfere by having common points while not saving them for duration of processing in higher priority code. This is not done automatically. Program has to do that itself. Interrupt should be considered random event and main program (or lower priority interrupt) could be in any state.

Many times this is just a human mistake ;-)


Also sometimes we forget about timings when processing interrupts. Some applications need their procedures to fit certain maximum periods of processing or otherwise whole cycle has errors.