Apparently, if you install Adobe Flash Builder Pro application, and then install Master Collection or an other Creative Suite that includes Flash Builder, the Flash Builder Pro installation will be reverted to Flash Builder Standard.
It appears the reason for this is that the installer for the suite, or maybe the serial number used, confuses Adobe’s licensing system and it ‘forgets’ that you already installed and correctly licensed the Pro version of Flash Builder.
Follow the instructions in Adobe technote 83941 to fix the problem.
Steve Howard's eLearning ++ Blog 