Wikimedia Bugzilla is closed!

I used a hook to create a new user using the AutoAuthenticate hook, permission
to read the pages had been disabled for non logged in users within
LocalSettings.php. The new user was inserted into the database but the
information was never committed.

Tracked it down to the following code:
$output->loginToUse();
$output->output();
exit;

When this happens there is never a call to $mediaWiki->finalCleanup so there is
no commitAll() to the database.