Just a dumb question, but do you have a brother? Could someone in your family have spoiled your game by killing your shop keepers while you were gone?

I would have thought that they would have made the merchants unkillable. Maybe it can be fixed.

On the bright side, you now have a place to store your stuff. In my first run-through I killed Balathor because I wanted to take all of the stuff he had for sale. I quickly found out it doesn't work like that and that shop was effectively done forever. It did respawn food on the shelves but that's about it (maybe sacks too, I don't quite remember).

So until I bought a house, I kept all my loot there. The only difference is that you can't sleep in the bed. It's "owned" (lame, lame, lame).