The Chemical Decomposer used to take compressed cobblestone at Double and higher densities, and since the last update, does not appear to recognize them. Now, it will only take the base level of compressed cobblestone.

Tempfix: place the compressed cobblestone in the decomposer and restart your game.
See: https://github.com/jakimfett/Minechem/issues/791#issuecomment-128198136