I am hoping they will fix this at some point. Most things I put on shelves and stuff stay after the first time or two I place them there. It's gotten to the point where I never place more than a few new items in my house at a time. There is also the issue that happened in Oblivion sometimes as well, where if you remove an item that "came with the house" and replace it with something else you like better, the game re-generates the original item which knocks your carefully placed item off the shelf or table or whatever. No matter how many times you move it or get rid of it, it just keeps going back where it used to be. And what's with the silverware? All those napkins and forks and knives you can't move. They clutter up the place and I can't even pick them up.
But has anyone noticed that books disappear? There were a couple of books on tables in my Markarth house. I didn't like the color of the covers, they blended too much with the table. So I took them and replaced them with more colorful books. The next time I came home, they were gone. Just gone, not on the floor. I tried it again, and those books disappeared too. Weird.