I browsed through the topics, because I remembered to read about a similar bug.
But I didn't find that topic so I wrote it down.
In a new document make a new layer and paint sg on it
Than make another layer and paint a little on it too (just for control)
Than change the layer order: put the newest layer below the firstly created
Finally undo before the state, where we created the second layer.
Not that will be undid, but the firstly created (now upper) layer will disappear!
Sorry for my bad english, I hope my procession will be clear for you.
And if this bug is already known by you... than just delete this topic. : )