I've experienced something very similar and recently. I took items from the bank, logged off, logged back on, and I noticed the items in my inventory were not the items I chose from the bank. It was like the "bank tables" between what my game saw and what the server saw were desynced. No items were lost, but it startled me a good bit!
I thought it was really strange since I have never before encountered lost items and such.
I noticed at the time it happened that my computer was uploading something, so my connection was really laggy. After closing that program that was putting stress on my connection, the problem went away. Maybe your connection is laggy as well?