So I've run into this problem before, upgrade VTProE and the green 'Run Project As' emulator does nothing. The fix was always to install a previous version of VTProE.
Just got a brand-new laptop for work, installed and ran MasterInstaller. VTProE has the same issue. I inquired with TB about this possibly having to do with Flash being discontinued and maybe it includes Adobe Air? I was told that the latest version of VTProE (6.2.02.08) installs an internal version of 'Harman Flash' (yeah, what else can they screw up?).
I was told to uninstall VTProE and SmartGraphics, download the individual files from the site and try reinstalling. Did that, same issue.