There was an 0.9.0? Sheesh, been so long ago I couldn’t remember.
First, the page not found stuff has nothing to do with the manager, so not sure where you were going with that. But it sounds to me like either some of the files didn’t get uploaded properly especially in the manager area, or the data structures are missing something (though I can’t think of any db changes to the site_snippets table off the top of my head).
Not much else I can say about it without access to the installation or more details about the problem. Not even sure I understand what you say it’s doing. Which main page is it redirecting you too? The manager home? Or the main page in the front-end of your site? If the latter, you definitely have some kind of htaccess or other configuration issue.
Finally, I’ve upgraded a lot of 0.9.2.1 sites to various betas in the last week or two, and never experienced anything similar to this, so I believe this may be something unique to your sites or environment.