This is a reasonably specific 'bug' but it is very annoying when you are not used to what happens!
So this is what i did:
found a discussion which had no tags on it, (I have quick tagging enabled through my preferences) and i type in a new tag and click 'Update Tags'. This added the first one and was visible above in the hypelinked text. (the box however was empty). I decied to add a second and typed it in the box, clicked 'Update Tags' and it adds the latest but overwrites the previsous one.
It was not obvisous that the box would replace rather than append as the current tags are not shown in the box (which I beleive they should be when one exsists)
If you navigate to a content item already with tags the box is pre-populated, and you don't get this issue, it is only when adding tags to something without any tags in the first instance.