Update again-
Turning off the_end at first did not appear to break anything, but apparently something with (at least) the transmutation tablet requires the_end to be on, because using the tablet only half works with the_end set to false in bukkit.yml. Item's cannot be targeted for creation in the right pane of the gui, but turning items into emc still works, and transmutation from displayed items in the right gui still works. Weird O.o