I set it up using batch files like Daphne. Don't have access to my cab at the moment, but I believe each batch file does the following:
-Launch joy2key (I have a GP-Wiz)
-cd to the specifc game directory
-Run the loader
-Start /wait a vbs script that keeps running until it sees game/launcher.exe exit
-Taskkill joy2key after the vbs exits
Probably not the most elegant solution, but it works.