Do you have SQLPATH set in your environment? In that case, you should unset it. It could also be a glogin.sql file in your Oracle Home that is causing the problems. Try to delete it.
Or - I can recommend you to try the new AutoUpgrade tool which is now our preferred method of upgrading. It does take care of issues like that for you (together with a whole bunch of other things). Check out the quick start guide.
I'll try the Autoupgrade tool - thanks.