This happened in SMP 1.7.5 and I thought I dropped the item and it de-spawned while I was afking. I was just in 14w21b and noticed something similar happen, not afking.
Steps, basically:
I had an item selected (specifically, holding the item)
I closed my inventory
I expected the item to drop to the ground; instead it disappeared
I repeated this about 3 times to the same conclusion
Again, this explains what happened in 1.7.5, but was tested in 14w21b as soon as I realized what was going on in 14w21b.
PS: I did a search to see if this bug has been reported, and I saw no matches to this (keywords: Item Deleted Inventory Closing)
The behavior you describe is the correct behavior for creative mode. But of course you said it's happening on survival, hence the "it's a bug" reaction.