MH-9 & UH-80 still at 30 meter at most time in that mission. Looks like only AH-99 defected.
Better point of view from ground - we can clearly see, than heli get active climbing to 1-st WP, then more climbing to 2-nd WP...
Video is here - http://youtu.be/f3Y8AV1LP7I

Distance in original missions across all west Altis with some WP and 20-30+km route length. In attached mission - around 10 km. Its must be enough for correct altitude management.
I am was set diff. behaviour (from careless to combat/stealth), move WP from mountain - it has no results. From any to any WP AH-99 is still climbing.

Setwind is limited. Ticket can be closed.

Fixed. Ticket can be closed.

Altis also affected.

"setTerrainGrid 0" fix that. Ticket can be closed.

My scrinshots was taken in singleplayer. Ultra settings, view distance at ~5km.

Fixed.

Same rock from another positions:
player setpos [3225.06,4662.7]; player setdir 128.541;

Look at 3 screenshot taken in strong wind environment:

1. tree at minimal angle;
2. maximu angle;
3. overlay from 2 previous screenshot.

Get a closer look at the last:
1st look at any far tree, leftmost etc. I am colored one of tree from right - green line for trunk in minimal angle, red line in maximum. Both lines converge at ground level (yellow line).
2nd look at closest tree. Red & green line converge not at ground level (yellow line), but 0.5 meter upper (blue line). Tree rotates in blue ciruit point, not ground level as any other tree.
This is root of the dancing tree problem.

Easy way to reproduce in your game - in debug console on Stratis:
player setpos [3164.84,4549.03]; setwind [30,-30,true]; skiptime 24;
We get storm and dancing trees.
One more video (speedy):
http://www.youtube.com/watch?v=tqC1_wTuIPs

And one more time - setwind must be limited in it maximum range. We can define any crazy value, setwind [-1000,1000] etc. and tree start fly on the sky as dry leafs.

Yes, my mistake. Scripts in some case set up much higher wind speed...
But maximum wind speed, which can be set up in editor is 10, but value has slow rise & slow fall. Some minutes to pass from 0 to 10.

To avoid such "dancing tree", setwind command must be hard limited in some range, -20 to 20, etc. Or fully described in wiki...

With this recomendation case can be closed.

You dont saw video, but start write something (i check youtube counter)...
In video setWind [10,10, true], as we can see at example: http://community.bistudio.com/wiki/setWind

But you dont see original problem - root of the tree creeping over ground.

Look at dark tree with white marks in center, and two more not far.
Thats very funny for alpha, and stupid for upcoming beta...