How did you run the upgrade? Did you run the commend using "profile install", or "profile update". "Update" may leave old - now unused - vibs installed. Unless you use additional custom drivers, you may try running the command using "profile install", which will end up with just the new vibs which are included in the profile, i.e. requiring less disk space.
Also verify the offline bundle's checksum to ensure that it's healthy.
André