In the server Infinite chest are not working good.
They are not taking the ems . like many time [eg- R-villeger farm]
some time takes ems
Thx
First use a version which allows chunck borders and see if the place where mobs are killed (the place where ems drop) and the ichest are in same chunk.
Then check if you have selected the correct variety of the item (you could have selected normal emerald instead of enchanted one)
If you have done all , don't worry it happened to me once, it will be auto fixed in some time just place some normal mob collecting drops for some time.
It will be fixed automatically, it's like a random error thing