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Strange since that shouldn't be the case. I have it after AEL_TilesetPropertyRegions because it's dependent on it.

That is strange.
Ahhh sorry, looking back between your new example and everything I was able to work it out after checking more things. The original 'working' wasn't working first of all xD; it was a left over layer from the original method of creating a region map matching the property regions, the one thing I forgot to check.
Removing that meant the bush I thought was working, obviously wasn't because as you say AEL_TilesetPropertyRegions had to actually be before it.

What I missed was the 'Tileset Name' property in KEN_TiledFlagsLayer. Renaming that fixed everything :)!