I have a couple of emulators that require that I map my gamepad differently for each. Using MameWAH, you can specify a program to run pre and post running of the emulator (awesome btw

Anyway, I know you can run joytokey from a command prompt and load the appropriate .cfg file specified. The problem is, if I type the contents of the batch file, it works fine. If I run the batch file, it hangs after it loads joytokey. Is there anyway around this? Has anyone else seen this behavior?
Thanks again for your help.