It does take a while to get those boundaries in place. It took me several months after I told W she was not sleeping in the same house as me before I took the house keys from her. She was coming and going as she wanted and it was not until she walked in the bathroom while I was showering that I felt my boundaries were being crossed. She was extremely angry when I took the keys but she settled down (most likely OM explained the facts of separation to her). Since then I have given her back a key for taking care of things when I was on vacation. She hardly needs to come to my house anymore, but will call me before she does and it is only to get things for the kids or to slowly get more of her stuff from the house.
