yeah it seems to be a bug with the world editor, i tried the same with the default world map and it was having the same issue, so not related to the world generator at all. odd thing is there are some prefabs (not many) that actually will show their default ground texturing when placed while the majority of them won't.You can edit the prefabs, but only BEFORE loading the world the first time.
The game will go over the original map, generating the "processed" files, placing things like road and mud textures.
If you delete all of them, the game will redo them, thus making your prefab look correct again.
(Editing the processed files, you can even remove the mud texture around lakes, if you can handle that specific TGA format)
back to the water issue, i changed the elevation of my map (shifting the elevation up 2 pixel shades) and the missing water blocks in the surrounding water area changed, not as much missing now so not sure if that is related somehow to the elevation. if it is, its a odd math bug as there doesn't seem to be any consistency to it. it does appear to be the same size as a chunk loading in at the edge of the 'viewable' area. noticed that when using fly and passing though the landscape.