This may be an issue with Atomic Science. If I attach a manipulator to Atomic Science machines, regardless of side, the manipulators will pull from or insert into both the input and the output slots. I'm forced to attach a hopper and chest to these machines and have the manipulator interact with the chests instead.

hmm i'll look into it it could just be the AS machine use the old ISideInventory system. Which i removed from the manipulators but it will still interact as long as the machine is an inventory.

This is most likely due to mekanism not supporting the new way inventories work. Ill look into it when I get home though.

same issue with the Mek Enrichment Chamber and Basic Factory. Confirmed with the Configurator that the output side was set correctly on the Mekanism machine. Confirmed that Buildcraft pipes could extract from the output side of the Mekanism machine, but the Manipulator on the same side could not.

AssemblyLine #142, Mekanism #76