Sometimes too many items spawn in a chest and some are lost due to lack of space to appear. Best example is the chest in Necromancer's Guild which contains Eclipse. Grayface's patch has a fix, if the chest was initially full, clear space in the chest and re-open it. Any items which couldn't appear the first time will appear if there is space.

Are the items neatly lined up the second time you open the same chest? If so, it is definitely the fix in action.