I don't know anything about the "missing chest" in the "tavern room", but if you're talking about the Sunken Flagon, the only containers in it are the benches in the back, and I use them to store my items, and the only time when items vanished from them was at the end of Act 1, when you-know-what attacked and kidnapped you-know-who. The issue resolves, though, as soon as we enter Act 2, the items returning into the benches. I'm guessing that the tavern during the ambush is registered as a different zone, thus the benches don't have any items on them because these are new benches, benches I never stored my items in.