As I designed and have played many levels with JA, it seems that sometimes, apparently randomly, sometimes a sound effect cue won't play when it should. Instead of the player jumping and hearing the jumping noise, it's silent. But checking the code shows there is a cue there for the sound effect, and any other time I play, it works jet fine. Maybe it's the high amount of events in the level? Has this happened to anyone else?

Actually, it has. If you cram enough events to where you aren't allowed any more, you can see problems like this. For me, I had a problem where an event wouldn't take off unless it was on touch. I wanted it on check, but changing it from touch to check would result in the event not working... changing it back to touch and it would work fine. All the conditions were never changed.

I think this is directly related to the number of events (or how much data are in said events) in one location. The only suggestion I know to fix this is to make rooms smaller so it wouldn't require as many events... and I would prefer that to say sacrificing something you want in you game but don't HAVE to have.