For some reason every mod offsets the itemId in the configuration file up with 256(Maybe to make place for the blockIds?), except EE3, which places the items at the ids it promises.
I believe this should be investigated, what's usual and what should EE3 do.

https://github.com/pahimar/Equivalent-Exchange-3/blob/master/ee3_common/com/pahimar/ee3/item/ItemEE.java#L21

https://github.com/pahimar/Equivalent-Exchange-3/blob/master/ee3_common/com/pahimar/ee3/lib/Reference.java#L23