I am having issues saving the craft after exiting the module screen, and when going back in it just displays a blank crafting space.
This specifically is happening with the Assembler

These are the screenshots of putting a craft in the module and after exiting and reentering

The wrench was messing up the craft, nevermind

Welp, it still isnt working :(

GTCE isn´t at fault here, the problem is between JEI and LP, if you drag an item from JEI and the use the scrollwheel to change the amount of said item, it isn´t going to be saved, so you have to have the item in your inventory for it to save. This bug is mostly fixed in the new version . Probably a bit late, but at least people with the same problem can see this and it will help them out.

Seems like a duplicate of #1612 and is therefore fixed in version 0.10.4.12.