I've never had this problem?
Helicopter flies about the same to me day or night, no matter the behaviour.
I also don't understand why you need an unload waypoint for the squad in the chopper. I have never used this, transport unload has always dropped off the squad fine, and they go to whatever waypoint assined, I don't think you even need to use the Unload waypoint unless your dropping off a couple different squads at different places.
That's just been my experience anyway.