If you're using SmartExec to launch an AppleScript file, that no longer works (same as BAT files on Windows).

I've actually been given the source code for Fire-Up by the guys at Atomik Software and I'm going to be releasing an updated version of their tool for the Mac (and PC) once I have the time to dig in and fix it.

Conquering FSCommand EXEC Part1 : Proxy contains the info you need to get your BAT files working on Windows again.