It just happened when we went to 2006. The company provides profiles to start with, then we can change them to suite our needs, which worked fine in 2004. They know about the problem, but it doesn't look like it is a high priority right now, which is why I did this work around.
To clarify.
Yes they use specific company wide profiles.
But one can change them, and in theory, have them remain changed until upgrade or you overwrite them back the the standard ones yourself.