I am having issues with the Molecular Assembler as well in Infinity. I am trying to hook it up to a Recycler to turn the scrap into scrapboxes automatically. I have fitted it with the pattern, but I cannot get any scrap to be put into it by a variety of mods... I can hand-feed the scrap into it, and it will craft and output the scrapbox to a chest/barrel as normal, but a recycler with an output upgrade, ender IO item conduits won't transfer scrap to it, buildcraft pipes won't (though the wooden transport pipe initially wants to hook up to the M.A. and output from it by default, which I found odd)..
I even went on singleplayer and rebuilt a setup and still nothing. I couldn't get it to take planks from a sawmill and output crafting benches, unless I hand-fed the planks to it, which kind of defeats its purpose.
I'm really hoping it's just a simple bug that will be fixed soon o_o.
