[NoggIt and Cryect Tools] Terrain acts wierd?

[Appled]

Hello there.

I have recently been starting to model edit. I know how to make mountains, edit terrain and stuff but I have never known how to add WMOs/Doodads to your area untill now. I have got NoggIt3 (works with wow 3.3.5).
I go to NoggIt and look for good place to edit terrain. I save the ADT, take it to fileinfo.exe and add one single WMO or doodad. Then I save the textfile and add it to loadinfo.exe. After that I drag the file back to World/Maps/ folder. I open up NoggIt3 and the ADT's terrain, where I added the WMO or doodad, has changed to darker.

Picture from NoggIt3!

EDIT: I was able to remove the dark part by saving ADT and restarting NoggIt3.
And then I made a MPQ file and insert ADT inside. Results ingame are the terrain has got darker, just like NoggIt shows, and loads of trees/doodads has disappeared.
Picture from ingame!
Also I am not sure but I think my doodads are not appearing ingame at all.
WMOs and doodad sets works although.

The best regards,
Appled of MMOwned

[Spitfire103]

if you go over the darker color terrain really quick with a smooth tool it changes it to the regular color.