Isn't there a box that you can check when that message pops up asking not to show the message again, or don't ask again? If you go into Tools/Options/General there on the top is the system defaults. You can check/uncheck the box to see if T-Bird is the default mail program, or you can click "Check Now", and see if E-Mail is checked as the default client, or check/uncheck the box to perform this check when starting Thunderbird. Fool around with it, and one of the option should work for you.