When signs with a clickEvent that runs a /give command is clicked, the item goes into the player's inventory, but does not show up until you reload the world.

To reproduce, type the following command into a command block, activate it, and then click the sign that appears. Reload the world to see the item it gives you.

Command:

setblock ~ ~1 ~ standing_sign 0 replace {Text1:"{text:\"text\",clickEvent:{action:run_command,value:\"give @p emerald 1\"}}"}

Upon further investigation, selecting the slot that the item should be in and pressing 'q' will drop the item. Once you pick it up (you may have to do this more than once) the problem won't occur the next time you hit the sign.