hmm I don't believe any of the chests I used came from the castle, however I am pretty sure the chest with the potions that somehow got linked was from Stormfist. They never disappeared in my inventory, just after I dropped them on the ground anywhere outside.
I had a house in the main starting zone until I grew out of it with my massive packratting ways. I moved into the Cursed Abbey pretty early in the game. It has huge halls to store my 50 chests all around, and close beds to sleep in. Also, it's rather close to a transporter.
One item I did have disappear on me was a barrel of poison. I had stacked 3 of them in my inventory and when I was messing with putting them in a chest one disappeared for good.
I'll test the invisible chest more tonight. I need to finish up the treasure map quest then do the Council ending too.
Side note: I took 8 years of German classes in High School and College... probably don't remember much about it being 6-7 years removed from college though...