Maybe we should remove the "Convert All Categories" button. I think people are clicking on that and then clicking the confirmation that follows when what they really want to do is selectively convert categories. I've been unable to make selective conversion accidentally convert all, so I think clicking the wrong button is what is happening.
If you already have a tag with the same name as one of your categories, you cannot convert that category. It will not show up in the list of categories to convert.
If you have categories that weren't properly converted to tags and no longer appear as categories, hit feedback and let us know.
We fixed some caching issues that were affecting the tag and category displays. If you still have problems with tags or categories not displaying as they should, hit feedback and we'll clear your caches.