I think it's (or not) a bug, but if you Save the map when trying to use Tile Cache (e.g. for Triggers in background) it won't really work.
Are you planning to add a feature to make Tile Cache stuff easier (Such as you can place Triggers in layer 8 and it automaticly places the Tile Cache tiles.)?

Also what about adding a shortcut for changing the tiletype to normal (e.g. making fog and want to remake it back to normal, then you have to spam rightclick, so what about holding e.g. shift+n to change all back to normal)?