Hi Jim,
That seems to be happening because the application is triggering a second interrupt while the interrupt service routine is being executed (and it already asked for the flags); therefore, it will be possible that just one of the sentences will be executed, clearing the interrupt flags after its competition, avoiding re-entering to the same interrupt by other flags.
So, as a workaround you could try clearing the interrupt flag at the beginning of the ISR, and maybe restructuring the logic of the code allowing multiple calls to the ISR without repeating the actions of a previously executed task.
Hope this will be useful for you.
Best regards!
/Carlos
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