Did you already try to accept this message and hit yes? If so does it still appear?
Yes, I click the yes button every time that I launch Bridge. It is always there to greet me the next time I boot.
It means some of the start up scripts have been messed up and usually means something wrong with your install.
I would first try to reset preferences with holding down option key while restarting bridge and choose reset preferences.
Also check in the Bridge Preferences what start up scripts are checked (ideally all start up scripts should be checked but you also have to have the according applications installed at your system)