I would need to see whatever you have got in terms of a configuration. I have never had MediaMonkey start by itself on any computer or with any version of VoxCommando, ever, unless I use a launch action, or try to generate xml for MediaMonkey.
If you want to send me a backup of your configuration, I will take a look.
As for your problem with VC "misunderstanding" you after an upgrade, I don't know what to say. You can always do a purge and restart to be sure there is nothing weird happening after an upgrade. Other than that, I think you are having a special experience. The core recognition technology has not changed, unless you use the SP version.
No, I have no idea why this is happening to you, because I don't know anything about your setup, but it is not normal behaviour as far as I know.