I didn't notice any such errors until I installed the Shivering Isles expansion a
couple of months ago. Now, every time I resume the game from a saved file, some items from my houses and my inventory are missing, and if I'm in a cave/mine etc. all opponents on the same level are gone as well. Reloading older saves does not correct the matter - it is as if the items have never existed.
Hopefully there's no limit in the game as to how many things you can "own" - I'm a bit of a collector of weapons, armor and magical items, and the amount of loot I've hoarded during my adventurous carreer is quite extencive...
Any suggestion to resolve the situation would be appreciated.