The crafting terminal isn't able to pull different ingredients when pressing [+] to pull down. It will only pull down what it is showing. I honestly thought it was REI but it also seems to be an issue with JEI as well. I tested it with a regular crafting table and even refined storage and Tom's is the only one that isn't able to do so. A picture of what I'm talking about(crafting a storage terminal for show):

Fixed in latest releases