Hi Way Of Time, the Ballad of Alchemy is not quite distributing items properly I have tried inserting the items in different ways but it still ends up looking like this and the redstone always stacks so i can't automate the creation of cataists. This problem is in beta v1.2.0beta18(1.7.10). Just wanted you to know that the problem is there don't worry about rushing to get it fixed I know you have a lot going on besides this little problem. =)

Its only when the player puts the items in the chests

Remedied in Beta23