I think it's because the scripting of the choppers doesn't take into account a number of possibilies. The use of eventHandlers in the CSJ UH1 config means that every time a chopper starts its engine another instance of the rotorwash script is run - the effect starts to look odd once there's more than one script running.
I've not spotted a universal off switch for the scripts - you'll have to make sure that once they've started their engines, they don't stop them.
Depending on what you're using the Huey's for, you could:
- make sure they hover 1 metre off the ground when loading / unloading troops. As a bonus, this adds atmosphere.
- delete and respawn them when out of sight