The base tileset is Ashenvale (For RealTextures I have), which currently is using 2 cliff slots. I read somewhere that if you use more than 2 cliff tiles, WE will ignore the rest. I tested this in a test map and it is true, I cannot place cliff tiles not from the base tileset via triggers (I can place via terrain editor)
I was thinking about extracting the tiles from war3.mpq and renaming them to a non cliff tile and using them that way, especially after finding out I can rename "name".blp files to match a non cliff tile set.
Thanks everyone for the help!