I tried to craft a Shot glass with the latest 1.12.2 version of Binnies mod and the Thermionic Fabricator will not allow the capability of putting the wax casing in the upper right hand corner to craft the nice glasses. Is there a way i can create a crafting recipe to do this, or can you fix this to register?

Yeah I got the same issue, seems they don't give a shit

I also am observing this problem. It is preventing from making any of the glasses (14 in all that I see currently in JEI). This also prevents any foods that are filled glasses of these items from being crafted (Fruit Juices, etc).

got the same issue on Minecraft 1.12, Binnie-mods jar 2.5.1.188

the glass doesn't want to melt also