I'm having the same issue today. Changing the pms_config.ini file has stopped Server2Go from shutting down, but is still running in my system tray when I close the browser. It also prevents me from opening another instance without shutting it down in the system tray manually.
Is there a way to shut server2Go down when the browser closes, or if I set KeepRunningAfterBrowserClose=0 is there another way to stop the browser from shutting down as soon as I try to start server2Go, i.e. prevent the original issue Brian, romapad and I have had?