While a player has a minium/philosopher's stone equipped, if said player sends some form of keyboard input, then this crash occurs: http://pastebin.com/1sNKVR1p. Doesn't happen for any other item.

https://github.com/pahimar/Equivalent-Exchange-3/blob/master/src/main/java/com/pahimar/ee3/network/message/MessageKeyPressed.java#L58 for reference.

This (missing handlers) is a Forge bug and has been fixed. I'm not sure which version fixed it. Try updating to to the latest Forge version.

Fixed since this commit MinecraftForge/FML@31d726a
Forge versions 10.12.1.1090 and above