And when you relog, that command block, is gone.
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Does it work on other blocks?
Yes, it does

Can confirm. Occurs with all tile entities, such as chests and beacons, so the title should be updated to adhere to that.
In the picture, you did not type "/" before setblock. It should be /setblock ...
It works for me, tested with several types of tile entities and air. All tests worked correctly.

@Andrew
You do not need to include the / for command blocks. You are using the latest snapshot, 14w04a? Are you using the "replace" method or "destroy"? It only occurs with "replace".
Ok, i changed it to Tile Entitys

Releated to MC-45041 (maybe duplicate)

Doesn't seem to have been fixed in 14w04b, issue still occurs with all tile entities. Any further confirmations?

Reopened, this is still an issue
I can confirm this. The block will disappear when you try to open its inventory

I accidentally found this with comparators.