it seems to be a problem with all systems. I'm on a PC.
From what I've been able to determine (and it's a WAG), the items like to revert back to where they landed when you drop them to put them on a shelf/table. It also seems to take a day or so. Possibly something to do with the respawn timers? I have placed items on a shelf and come and gone from my house a few time in one day and nothing has happened. Go away a few days and bam they're on the ground again. It could be thieves I guess, since we can't lock the doors. lol.
The one exception I've noted is that journals and notes seem to stay where I've put them. Most of the time on the shelf. I don't know, I just like stacking the little journals up color coded
The notes I've left on the shelves are mostly the treasure maps that I've found and the paperwork for Frost. All the others, bounties and death threats etc I've stuffed in one of the sacks.
On an aside, when you decorate your house, do you leave all the junk that came with it, dishes, tankards, jugs etc? While it looks nice, to me they're taking up valuable space to store things
I collect them all up and sell them... or if I'm really lazy and there's a barrel I haven't used, I stuff them in there. Sometimes I just take them to a barrel outside the house and stuff them in there and let the respawn timers clear them out. Kind of like trash day