It sounds like it is an issue with the SumTotal Plugin.
If you publish normally to SCORM 2004, or 1.2, items 2, and 3 are not a problem. (Just make sure you enter in the description when publishing, and make sure the AU properties are set for the correct mastery score)
I know that with SCORM 2004 with one client, we have had to manually edit the manifest document on every publish to get it to work on thier LMS. So I’m not suprised to hear this at all.