Holding middle click while crafting does not use the Pick-Block function... What is supposed to happen is for example if crafting two crafting tables instead and using right click and go over each spot twice if you have 8 wood you only need to go over each spot and it automatically puts 2 wood in each spot.
Using right click instead would waste time and I do use the middle click feature quite often but now in 1.8 i cant.
Had this problem in a multiplayer server I host. Was unable to fix through setting the affected players spawnpoint. Eventually had to manually delete their .dat file to allow them to keep playing.