The atomic reconstructor does not turn bone meal into ink sacs as listed in the recipes of NEI, and its tedious to find squids and then get a good amount of ink sacs. I do believe this is a glitch that needs to be fixed as I have checked banned items and nothing like this was listed, so that is why I am asking it would be readded or fixed.
Use the black flowers found anywhere if you can't get it to work. I've confirmed that it works though. Maybe you just forgot to use the correct lense?