Is beta3 still tagging twice when running manteinance tool? I can't test it now because I'm moving to another hosting.

It shouldn't. Nobody confirmed this yet.

One thing I noticed with Beta3, as the admin, if I edit the tags and remove some, when someone replies to a post, it adds those tags I removed back again.

This is by design. If you don't want this you will have to disable the plugin that hooks in "threaddata_postsave".
Another solution is to include that word on the bad words list.

It says 200 were tagged. Nothing was tagged though. Now it's working perfect for threads that are mad normally. Just the RSS aren't receiving tags.

Finally it's finished, v1.1 is GOLD. Main additions are tag proposals by AJAX, tag by scheduled job, tag RSS threads, tagging after thread title changed, add thread prefix as tag. Also there are many fixes and other smaller changes:

History
1.1.0 GOLD, 31th July 2008
- Added tagging by AJAX. If enabled, tags will be added to the tag field after leaving the title field. There is also a setting that controls the availability of that feature and also controls if leaving the title field will erase all tags entered by the user.
- Added cron to auto tag not tagged threads in the night. Please run maintenance auto tagger before this to tag old threads.
- Improved overall process of tagging
- Tags that were added via new thread process, RSS or maintenance are marked as autotagged (this does not count for AJAX tagging) and can be removed
- No need for editing rssposter.php anymore. RSS Feeds are beeing checked via maintenance or cron.
- Fixed Smart Tags for existing threads
- Obeying max tags limit while creating a new thread
- Tagging thread also after changing the title
- Stripping of HTML and BBCodes
- Possibility to add thread prefix as a tag
- Fixed not tagging threads if tag limits are set to unlimited (0)
- Fixed problems with other languages. Please keep in mind to replace the filter replacement '&'=>'and' with ' & '=>'and'
- Fixed problems with duplicate tags and enabled "Disable Auto Tag if Tagged?"
- Removed exclude Usergroup setting
- Maintenance Auto Tag Threads has now the possibility to hard-delete all auto tags prior to new tagging. With this you can skip the Delete Auto Tags step.
- Smaller fixes and changes

How to upgrade?
Just overwrite all files and re-import product XML, overwrite.

This has been improved in v1.1 GOLD. Now such threads with not 'tagable' titles are filtered out.

Thanks for the update :)

What do you mean not tagable?

I just upgraded and ran the cron. Still nothing. It's not tagging the RSS feeds.