I don't think there's any difference in the Guest Additions, but VB will sometimes nag if the version of the GA doesn't match that of the application. It seems to be a simple string comparison, so you'll get nagged when the software is identical apart from the edition part of the string. I've never found any mismatch between GA and application functionally, even over several upgrades of VB, so I suspect the GAs tend to stay the same most of the time, whatever their "version".
As for the problems with shared clipboard, that's a long-standing known bug in VB, which they might get round to fixing one day...