I had this same issue. I do not have auto-loot enabled. I would try to open any supply container (anniversary, crafting writ rewards, Dark Brotherhood rewards, etc), and it would come up blank. Basically you'd go to open it and the menu changes to reflect that, but there are no supplies visible. I also couldn't close my menu unless I hit the start button. Sometimes it would take restarting the game multiple times to finally collect my items, and other times I just left it for hours before it finally would open. I haven't tried opening a package since April 14th, but it was still happening then.

I also placed a ticket in game for this issue sometime last week, but haven't heard anything about it.