On dungeon level 10 I picked up a suit of crummy artifact armor (a variant of embossed serpentine plate), which I meant to send to the museum for experience. However, I accidentally selected the skill Lucky Pick instead of It Belongs in a Museum. When I right-clicked on the crummy armor, it switched with the nice armor I had been wearing (as normally happens when right-clicking a wearable inventory item). The nice armor, though, didn't appear in my inventory or on the ground; instead it totally vanished. My inventory was full at the time, which may have been a contributing factor. Snow Leopard, Steam, 1.0.10, RTDG, no mods.
Sorry for the late update. I can't reproduce this, unfortunately. I have tried with full inventory also, but it doesn't disappear for me.
Sounds like the items stacked on your body. When an item gets stacked and then equipped, it sets the stacksize to 1.