Are you using hyper triggers? Any other waits in OTHER triggers that are running at the same time? If you are using hyper triggers, the level 'pauses' for one second because the hyper triggers just had the usual 'cooldown' pause. I forgot the official term for it.

EDIT: I checked the Glossary, and the term for it was NEO. (Next Ending Occurance)
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If you use even 3 hyper triggers NEO doesn't happen for hours... right?