This just comes to mind. But if you use the PCSX2 Configurator plugin you probably have to remove it from the LaunchBox plugin folder. I noticed the PCSX2-QT versions uses a slightly different command-line syntax. Previous versions use -- before an argument (example: --fullscreen), while the QT version uses - (example: -fullscreen). So your old PCSX2 command-line parameters in LaunchBox or per game custom command-line parameters won't work with the QT version.