After reading about alot of people encountering the non functioning rack glitch, and experiencing it myself (Breezehome-Xbox 360), I decided to do an experiment. I purchased the home in Markarth, Vindrel Hall, and bought the upgrades first one at a time then all at once on seperate saves. I may have found the answer.
On my first purchase I bought the home, went and checked it out then returned, saved and purchased the living room upgrade. I had a glitched mannequien. >( So I reloaded and purchased the home and all of its upgrades IN ORDER before going to the house for the first time. Bam! Glitch free! Btw none of my weapon racks worked in Breezehome, not sure what order I purchased that stuff in. Hope this helps some folks having these issues.

I purchased Vindrel Hall and the upgrades in order last night. Everything worked. Went and put Ebony Armor on the mannequin, Blade of Sacrifice in a display case, Blade of the Reach on a a weapon plaque and some books on the shelves. Loaded that save up today and wondered "why are some rock warbler eggs rolling towards me?" Cast candlelight and saw that almost all of the shelfing was gone or invisible, the alchemy table was gone and ALL the [censored] in my house was on the ground. Reloaded the same save and it was all normal, but for how long? When I leave to go quest and come back will it all be [censored] again? Seems pretty likely.

Do NOT load manual saves from houses, gets rid of upgrades. Try it, your auto save reloads it fine

I have the same issue with all my furniture disappearing. It only happens when my save is in the house. Reloading the save works to fix it and it stays that way, until I load a save, while in the house, again.