Below is screenshot of multiple triggers in flow manager.
What happens if you use the "arrives" condition rather than "exist"?
User not willing to change the condition from exist to arrives, due to below reason.
If it fails to trigger on arrives, it won't run.
Am I correct in assuming you are using the LSF scheduler? I don't see any option for limiting the number of exist checks. I'd suggest tracking the problem to Tech Support if you haven't done so already.
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