I like using the long pulse mode, not for any sort of wave action but to change the direction of flow. Of course this is only possible with multiple vortechs.
Although I'm starting to see diatom(??) growth on some of my corals, specifically ones that are large plating/tabling type (efflo, cap, etc) I don't know if its water chemistry or maybe an issue with flow now (damn corals grow in the way!)