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What version number is listed in the reference.xml's?  For the message to go away the version number has to be the same as mediaportal (1.0.0.0).

Also after running MP a couple times with that message, you'll be given an option to not be shown the message again.  Try restarting the program a couple times until you do.  I see you're running vista, so it might be a good idea to run MP as admin when you check that box, as to be sure the option is applied.

Give it a try and let us know if it works.  =)