OK, the lack of an application group is probably the root cause of your problem, and it's probably caused by having picked up a snapshot from CVS.
The code that creates the main site's application group is found in acs-kernel/sql/*/acs-install.sql. It maps "registered users" to the membership application group for the main site.
It didn't work this way prior to 4.6.1 - upon mounting acs-subsite would create its own membership group but no one belonged to it, not exactly useful for the main site's membership group!
I probably committed pieces of this work incrementally and you probably had the misfortune of picking up a CVS snapshot during that time. I didn't write upgrade scripts to move the old-style main subsite application group go the new-style because doing so would probably break any customization someone would've done to try to improve subsite membership stuff (and I know some people have done this.) Leaving it the way it was for existing sites didn't make it any worse than it had been.
But you probably picked it up at a time when I'd removed the old-style application group for the main site but hadn't yet added in the new-style.
You can probably figure out how to patch up your existing site by studying the acs-install.sql script I mention above.
