Board Thread:Questions and Answers/@comment-1661144-20130703062850/@comment-11577914-20130705230052

If I read your topic right then this should make sense to you. If not, disregard it :)

Put a chest directly next to your Autocrafting table. Put a minium or Philosopher stone (which ever one you're using) in the chest. That way when ingredients come into the Autocrafting table, it will use the minium/P-stone that is in the chest. You will have to keep putting minium    stones/P-stones in the chest every so often because they will run out of durability.

This is the method I have been using and it seems to work fine with no bugs.