My mistake -- that documentation is incorrect. The 3rd step of looking in the install path no longer applies (since v6.0). That was a compatibility holdover from VBP v4, but the v6 install will instead copy any such files to the %ALLUSERSPROFILE% location when upgrading from earlier versions.
This was actually by design, since non-admins don't have permissions to modify files under %ProgramFiles%, and Vista will make it very difficult for apps (even started by an administrator) to write to files there [1]. We'll update the docs to be accurate.
By bootstrapping, I simply mean the first-time initialization process performed on a clean box (in your case, dropping the files in the install path). This process could be manual or automated. One option would be to drop the files to
%ALLUSERSPROFILE%\Kinook Software\Visual Build Professional 6
rather than
%ProgramFiles%\VisBuildPro6
[1]
http://www.microsoft.com/technet/tec...k/default.aspx