One of the guides for noggit (sorry author I don't remember which) explains this. The tile you can't paint over has already got 3 textures layered on it. You can't add more than 3 textures to a tile.
I haven't bothered painting much since it's a really heavy job and tbh I'm a useless artist. But if my memory serves me, if you ctrl+click on that tile it will remove every texture added to it (leaving it white). Freeing up all 3 available layers.
The tile you can't paint over has already got 3 textures layered on it. You can't add more than 3 textures to a tile.
I dont know if you've got it wrong, or if its in the newer versions, but from now on, there can be a maximum of 4 layers on 1 chunk![]()
It's 4, not 3 layers. allways been like that.