Minecraft does not respond after tabbing out then back in.

While Minecraft is open (in a game, not the launcher) I tab out to go onto Skype or Chrome etc. and then when I come back to Minecraft it says it is not responding, I can't click any buttons in the Minecraft Menu etc. However, for example, if I was on a server people, mobs, and chat etc. all continue as normal, if someone destroys a block I see it, but am still not responding.