Ok, let me try to explain.

A few weeks ago we decided to change our CMS to Joomla. We used PHPNuke before. I made a simple script to export/import our nearly 8000 users into Joomla.
That works fine. But we had unexpected timeouts while page loading. We can't find out the error until our hoster locked the MySQL DB. The SQL I postet above caused query's what runs somtimes over 200 seconds and examed over 1 million records. I think this query is used during the login and runs dead everytime a user tries to login with an unknown username.
Because this we decided to update the Joomla Bridge to fix this problem. After the update it seems the bug is fixed. But new user accounts are not replicated from Joomla to SMF. (The other direction don't work too). A manual verify of the sync state shows "in sync" but it isn't!
For now we deactivated the registration because we don't want to downgrade the bridge.

I am not sure I have understood your problem.

1) New users register but they are not synced to SMF?
New users should be synced when they first login, not when they register. Have you tried using SMF registration? (and not Joomla's).

2) Existing users cannot login - are not synced to SMF
Maybe the script you made missed some value and the bridge cannot sync them? You can try manually copying all Joomla users to SMF using another script.

Generally the good idea would be to get a copy of the sql and try stuff on a local server, not directly on your host. Some hosts have very low timeout times for PHP scripts, so its hard to do conversions like that.