I have the same problem. Even though I choose to not automatically update, each time I restart my computer, it reverts back to the default of auto updates. The only way for me to keep from auto update is to start steam in offline mode, then make sure I click do not update game in properties. It is still a pain to do this, and have forgotten about it, and have been auto updated, the last couple of times.
For some reason, STEAM application doesn't apply the settings when it quits..