Not sure, the only mention of a problem like this I've seen is someone saying they dont use the game's player-owned houses because thieves can steal their stuff. Never had this problem though...
I am begininning to think that no one has had this problem, except me. If there's a thread for "weirdest glitches" (other than the famed "backward flying dragon") then this certainly falls into that category. I have checked for similar threads on all the Skyrim forums ... and I found one other player who mentioned about his Markarth house being "ransacked", but everyone there thinks it's a glitch. So it seems to be what it is ... a glitch, and NOT anything related to a quest.
Oh well, I'm stuck with a house with items scattered and "knocked over". I mean really, every room has things knocked over, and on the floor.
I know about the weapons rack's not working in other houses, and certain "personal items" that people try to place on shelves and then later being lost or knocked over. But I haven't "touched" anything in my house other than switching out weapons and armor (and those racks work in my house).
At one my point, my enchantment table was GONE (when this happened, I reloaded the game), and that room was a complete mess. Strangely, all my weapons on the racks were intact.
WARNING to Markarth house owners: beware of the phantom whirlwind, this could happens to you.