Same issue here. I bought a license today and now I have this frustrating issue.
I can start retroarch from the commandline without a problem:
retroarch.exe -L "L:\LaunchBox\Emulators\RetroArch\cores\fbneo_libretro.dll" "L:\LaunchBox\Games\Arcarde\..."
In launchbox nothing happens. I additionally disabled the "hide console option" to examine the output but it did not open.