The Problem:
When using a typical /fill or /setblock clock with commands like /clear or /replaceitem the inventory doesn't update visually.

How to reproduce:

• Open any world with minecraft 1.8
• set up a /fill or /setblock clock (bug doesn't occur with slower clocks)
• add a commandblock to the clock with /clear @p
• at first it seems to work, the items out of your inventory disappear, but now pick any items and put it in your inventory. The commandblock output says it cleared your inventory (the output in chat, hard to see ofcourse because of the fill / setblock commands executing so fast) but the items still appears in your inventory: http://i.imgur.com/2T4fmMq.png
• Inventory updates as soon as you try to do something with the items or upon relog

Same works for /replaceitem, but only when you take out the items of the slot it's placing items in ~2 times fast after eachother.