Well, you are hiding her stuff. She remembers where she put it, but it isn't there any more, because you've moved it to where you think it ought to be.
You could stop this by simply not touching her stuff.
Okay, I'm kidding a little bit. But it sounds like you have a system that works for you and she has a system that works for her. Your attempts to integrate your system into her life aren't working very well for her. And that leaves you frustrated.
I guess my question is, does she leave her stuff around for days on end, or does it get moved/used on a regular basis?
If she's leaving her stuff around for a long time, what I'd be tempted to do is clean the house and then take pictures of the neat, orderly, clean rooms. Then don't touch anything of hers for two weeks. Take another set of pictures of the rooms with her stuff lying around. Show her the pictures. Sometimes people can't see the clutter in real life, but they do notice it in pictures.
You could also point out at that point how much more difficult it is to clean when all surfaces are covered in stuff.
And then maybe work out a compromise. Off the top of my head, you could agree that things that both of you use, like cooking utensils, the vacuum cleaner, the dog leash, books and DVDs, should always go back to the same place. You might need to label hooks and shelves and bins to help her remember what goes where. (I live alone and I need to label drawers and bins--it helps me a lot.) But things that mostly belong to one or the other of you, like her coat, your car keys, your baseball glove, her blow dryer, can be stored in ways that work for the individual.
But to keep the clutter corralled, she can't leave stuff just everywhere. Perhaps designate a space in each room that will be her dumping ground, a chair in the bedroom, a corner of the desk in the study, a box on the floor of the front hall closet. Her stuff will be somewhat contained and your stuff and shared stuff will be where you need it to be.
Also, work on making it very, very easy to put stuff away. Even though I want to have neat, clean surfaces in my home, if it's at all difficult to put something away, I tend to leave it out. So maybe brainstorm together on how to do this. You hang up your jacket on a hanger in the coat closet, but she has a hook on the back of the door. Take the cover off the hamper so clothing can just be tossed in, instead of having to walk over to the hamper, lift up the cover, put the clothing in, and replace the cover.
It is going to be very hard for her to change her habits, especially since they have worked for her in the past. I'd start slowly, maybe with just one thing, like putting keys in a specific bowl every time she walks in the door. After a month or so, when that's become a habit, she could work on putting her coat away.
But remember, you are trying to impose your system on her. She already has a system that works well for her. I'd try to come up with something positive for her about learning your system. We all work better when there's a reward to be earned.
