What do you mean by "can't do anything as root". Please be specific about what you are trying to do, how you are trying to do it, and what errors you received. I've had no problems with su or sudo even with the earliest alpha releases.
Which build of VL6 are you running? Is it Standard or Light? Which version? If it's standard you should be running Release Candidate 1. If it's light it should be Beta 1. If you're running something older than that you probably need to install the most recent version.
What, specifically, isn't working in vpackager? Please post specifics about what you're trying to do (build from source or build from port, which application) and what errors you are receiving.
With a bit more information someone will be able to help.