Hi, John,
Yes, I can duplicate this issue if, after I change my User Preferences, I just exit CQ again without opening any other CQ function windows.
For example, if I make the User Preferences change, then open/close the Customer window, open the Quotes window and open/close a quote, I can log out of CQ again and when next I log back in it remembers that CQ and MC shouldn't display in my Adagio toolbar.
Please give that a try as a workaround for now.
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Regards,
Softrak Tech Support