Hmm.... Sounds strange, but I noticed that too... But as I said, is seems that if two consecutive GLs are too far away from eachother, the chopper won't take off. In fact, if they are too close, it does exactly the same... I think.
It goes beyond my skill to bypass this... Sorry...didn't try the DisableAI command though...
Edit: it's possible that the line :
@getpos _heli select 2 < 1
makes trouble, because the chopper's altitude must go below 1 before waiting _waittime. In some cases, if the ground isn't flat for example, altitude can be equal to 1 or even superior although the chopper has landed. I changed that line to :
@getpos _heli select 2 < 2