I have not found a resolution to this in the forums so far. Before upgrading to 2.3, I used Simple Tagging. I opted to have my tag slugs use _underscore's and not -dashes. When I imported them into 2.3, it converted them all to -dashes for me. I only noticed as I was suddenly getting all these 404 erros.
After not being able to find a resolution I did the painful thing of renaming all the tags using one of the tag managment plugins, and decided that from now on (until an _underscore option is added to a plugin or 2.3 core) I will use the Advanced Tag Management plugin to add new tags as it allows you to specify the SLUG.
Now if I manually add a tag by typing it in, or by using Click tags etc, when I hit save it creates a duplicate tag, now with a slug that has a -dash.
If anyone can help get this resolved it would be much appreciated. At present, I have to manually add each tag to each post using ATM plugin otherwise it all falls apart.
Also, when 2.3 displays the tags for a post, it no longer uses the tag name, but uses the slug. So dual word tags are displayed as word_word and not "Word Word". This is why there is an issue, all the other plugins add tags by their name, not their slugs.