Yesterday I bought a house in Windhelm. I've been saving up a while so I could by all the furnishings from the house. I went to my house and started decorating it. When I loaded my save in the house in noticed 4 major glitches.
Firstly, the most noticeable one, is that a display case i had filled with gems had decided it would be a good idea to spew them out. A good half of them had been dumped on the top of the display case and the two eyes of the falmer had been stuck in variouse places. The first was lodged half way in the wall and the other was floating in the air (after some thought I think this is because I overloaded the display case).
The second is armour manikins. When I went to put my dark brotherhood armour on one, elven on another and nightingale on the third, my manikins became invisible. I discovered if I put something else on the manikin it can equip aswell (like a ring) and then take it back off everything becomes visible. I also discovered my manikin I put elven armour on has an additional glitch. Its that each time a go into the house it has a blades helmet on. I now have 3 of them so this could be a possible cloning glitch (I put a blades helmet on it when I was doing the thing to make the manikin visible before I new rings work aswell).
My third glitch is weapons in racks. Firstly on one of my wall plaques with sword and shield, my shield has disappeared and I can't put a new one on. Also when I put the mace of Malog Bal in a display case weapon racks and loaded my save it was jutting out into the wall. My final problem with weapon racks is that I cant put the wabbajack or wuuthrad in any weapon racks properly; the wabbajack either floats in the air or sticks out on weird angles and wuuthrad is just depositied behind me. I also noticed it has a little fit each time I try to put in a two handed weapon, not just wuuthrad.
My fourth and final glitch is that bookshelves do not work properly. Firstly it sometimes doesn't allow you to put books in the shelf and secondly if you put to many boks in the shelf they all seem to dissapear.
I do have other minor problems like objects I've put on desks and the like falling onto the floor each time I come into my house but I don't think that is major glitch.
Anyone who can shed light on one of these problems, add anymore of there own or could help develop the cloning glitch, comments will be welcomed.

You should really break your endless wall of text into bullet points. It is a mess. That said, I did notice one particular glitch that isn't really a glitch. The "empty" room in Windhelm is indeed an extra bedroom. You will get it filled in when you become Thane to Windhelm and get a house carl.

Thanks for telling me how to get the room and for the tips. By the way I have confirmed that the manikin is cloning helmets.

I am Thane in nearly all the realms and have four houses... trying to buy the one in Windhelm but my "Blood on the Ice" quest is glitched and won't launch. No hope for Ps3 until Bethesda patches for it.