First off, I want to say that I know that this belongs in the plugins tracker, but I don't have ticket_create access to that Trac, so here I am. Second, can we please get an "0.9.1" version option in this main tracker?
That said, when the Folio plugin is set to "track_logons", it can actually interrupt the normal initialization process. What happens is that the $mod_init code from includes.php is called, and things run fine until it hits Folio. Then if Folio is set to track logons, it actually calls authenticate_account() on its own. It seems that a plugin should never do this, especially not during init().
I noticed this behavior because I am using the LDAP authentication with new account creation. I was testing out the newuser plugin and couldn't for the life of me figure out why it was never getting called. As it turns out, Folio was doing the authentication before the whole system was initialized: any plugin that got loaded after Folio didn't get to add itself to the event_hooks array (or $functions, or anything else for that matter). So my new user was created, but the newuser plugin (and my own plugin) weren't yet initialized and registered to listen to user creation, so they never got called.
I'm not sure of the best fix to this that would still allow Folio to track logons. Perhaps a user:logon event is in order?