I've been having this issue for a while, and can't seem to narrow down a specific cause. It seems to be something time-based, and it has even happened while processing a stack of items while I had the UI open. This didn't update the GUI, but when I closed and re-opened it, it was in plate crushing instead of etching like before. Someone on the curse page seems to have been having the same problem, so I figured I'd put this up. It isn't whenever you close and open the GUI, and it hasn't actually cut a process off partway. It's only swapped mode right after a process finishes, causing the next to not run due to the wrong mode.

The cause is same with some of the previous metal former errors -- NBT reading/writing. Already fixed in 1.0.1.