If you put emeralds in the market and look up a recipe in JEI your emeralds vanish.
This happened as i was looking for the best seed oil nut.

JEI version: 4.8.5.146
Pam's Harvestcraft version: 1.12a

I played the Modern Skyblock 2 Modpack

Id like to add that when closing the market the emeralds you have in it also vanish.
Possible mod conflicts in the Modern Skyblock 2 and 3 packs.

I also experienced this bug, if closing the market while emeralds were still in it, the emeralds disappear.
I'm using my own custom modpack (includes JEI), for which I can provide a modlist if requested.
Pam's Harvestcraft version (1.12.2zb)

This is still happening as of the Kidney Stone (ouch) update.