Uh huh. You wouldn't happen to be the arch mage, would you? And this chest wouldn't happen to be the one conveniently placed next to your bed? The one that will make a duplicate of any single ingredient you put in there, but will destroy everything if it's left in for too long?
If you isn't, and you didn't put all your stuff in the Magical Radioactive Happy Fun Chest of Nuking-Your-Stuff, then I don't know. I thought Oblivion tracked all your stuff and made sure it wouldn't be destroyed by neutral junk placements, but I'm not sure. Long time since I last played.
If not, and the chest was in a relatively public place, it might be that your stuff ended up getting overwritten by a natural junk spawn for that container, in order to make it seem more "used" (what kind of batshit crazy mage puts tongs, a broom and three rolls of yarn in a barrel? How did he even get the broom IN there?).
In that case, I'd just have to tell you to get your own damn place to store junk. There's a nice manor out West, can't remember the name of that coastal town... Anyways, a guy will sell it to you for a too-good-to-be-true price. Accept the price and stay the night. It looks like hell, but after the quest you'll trigger by sleeping there it'll be fixed up and cozy. It's actually my second favorite house, aside from Rose-whatsit manor in Gobbledegook (very long time since I played).
If you prefer, I think there may actually be a cheaper shack in that swamp-town down South. It's way out of the way to be useful as a resting spot between most quests, but it's affordable and actually rather thematic.
EDIT: Ninja'd, but I have a superior amount of words in my post. HAH!