Sometimes when I hit Publish All Customizations, I notice that the process doesn't result in the expected outcome. At first, I blamed my forgetfulness but finally, I took statistics. There is something wrong with the publishing facility. I even have a short screencast to prove it!
What am I doing wrong?!
You are most likely not doing anything wrong. I've see that behavior quite a few times. It started with RU11, I believe and it's a bug. It appears seldom and has (most often) to do with importing a solution from a lower version of a roll-up, as far I've cared to regard it.
Just to make sure we're talking about the same phenomenon, see my blog if you recognize the signs from the screenshots.
Short remedy - hit the button again. It always works the second time.
Long term solution - wait until Microsoft fixes it.