This item from the known issues list:

# NEW: Items in ingredients bags are sometimes "invisible" when logging back in. This is a display issue only; the items remain in ingredients bags.

Actually affects all containers, not just ingredient bags. I first noticed this on one of my quivers. Holds 6 types but only 2 types were showing. I took one out and the rest all showed up. I'm not sure if it affects collectable bags but I think it also affects gem bags. I don't look in the gem bag that often though so I can't be sure.

Oh, and while I'm on the subject of quivers. Were you guys aware that auto-reload is taking 2 stacks of arrows out of the quiver? One goes into your arrow slot but the second stack drops into your inventory. After part 4 of the Shroud I have to stop and hit gather to clear up space, there is normally an extra stack or two of silver arrows in my inventory. If wait till after part 5 there can be 3-5 stacks of 100 silver arrows laying around. I first noticed it when I returned to the game around the time U10 went live, maybe before that. I have NOT bug reported it.. the bug report window has never gotten along with me. Either the one in game or on the website.