I just saw this happen last night for the first time. I cleared a monster zoo and received an embossed serpentine plate mail with a couple of extra enhancements as a reward. I immediately swapped out my existing normal version of the same armor with the reward and continued on. Later on the same level I found another set of regular embossed plate mail. When I picked it up I hit the right mouse button by mistake which of course swaps my current armor with what I am holding. The problem is, when the enhanced armor was placed in my inventory it stacked with the existing normal armor and the enhancements were immediately lost. Not the biggest bummer in the world, but still enhanced items should not stack with normal items.
Seems like really the glitch here is an enchanted item that doesn't get a special name when it's clearly an artifact. If it had it's own name, there would be no stacking problem.