Using Mountain Lion (10.8.2) on a MBP (13" mid-2009) I have times when applications launch during startup even though they have been exited before the last shutdown. This seems to happen on the order of 10% of the time. These are not applications that have been set to automatically run on login.
When it happens, the restoration includes all the application from some given time...perhaps 30 seconds before shutdown.
If I were guessing, I'd say that the system takes snapshots of what's running and sometimes restores from a stale snapshot but I haven't heard of anything like that.
Any explanations or fixes?