A lot of people have a problem with grass textures not updating correctly.
This fix will make your animated grass behave correctly in the CK, as well as in-game.

This is confirmed working!

Open up both Skyrim.ini AND SkyrimPrefs.ini and at the bottom of the [Grass] section add/alter this:
bAllowLoadGrass=0
bAllowCreateGrass=1
bDrawShaderGrass=1
Then, in the skyrim installion folder open SkyrimEditor.ini and at the bottom of the [Grass] section add:
bAllowCreateGrass=1
bAllowLoadGrass=0

After doing this, the grass in the cell you are editing should automatically generate correctly.
Kudos to Mikanoshi and Yodude12 over at Nexus for this fix!
http://forums.nexusmods.com/index.php?/topic/556001-deleting-landscape-grass-lol/page__view__findpost__p__4660144

I suggest turning off grass animation (press '8') when not texturing the landscape though, seems to slow down my machine a lot...

Excellent! I've told my mod's users who had this grass problem to try this solution and one already reports it worked like a charm. Thanks for spreading the word about this method.