It's only been noticed for a Month now. Might have been when Bukkit changed the BlockFace code. I also wanted to wait, i thought you may have already knew about it and didn't want to waste my time or yours.
Things like Pistons, Stairs, etc. don't regen correctly.
Some things are now duping: like PressurePlates
I guess I could change the configs to not allow those Blocks but I'd like to see what you had to say about this. I'm sure there are more Blocks that need looking into it.
I would like to add double chests contents to the list of things that dont regen properly.