JER works fine in normal JEI, REI Plugin Compatibility + REI, but it seems to not work on EMI+JEI. According to this issue emilyploszaj/emi#196 (comment), when EMI is loaded alongside JEI, JER crashes JEI's mezz.jei.api.runtime.IJeiRuntime.getIngredientManager() and prevents EMI from reading extra recipes from JEI.

This happens only when you load a save the first time, but if one exits to the main screen and re-load the save, error goes away, and other recipes load normally, though JER still fails to load.

can confirm this is really happens