This seems to be a craftbukkit bug. Doesn't happen with vanilla server, but does with craftbukkit with no loaded plugins.
Ah, just tested again, and this seems to only happen in multiplayer.
I've come across this bug too. Steps to reproduce:
In creative mode, give yourself a command block (`/give username 137`) and place it. Note that middle clicking to pick the command block will work so long as you keep the command block from /give in your hotbar.
Next, remove the command block from your inventory completely. Middle click the command block you placed to pick the command block. It will appear in your inventory as normal but when you attempt to place it, it will disappear from your inventory and will not be placed. If the hotbar slot containing the command block was not empty before the middle click, this will instead place the previous block and revert to it in your hotbar.
This does not seem to affect 14w07a, but I did not test previous snapshot versions.