I don't see a reason for that to happen. What program do you try to open?
What happens if you run an empty script with just that line in it?
Run, %A_WinDir%\system32\notepad.exe
You only need the second parameter (working directory), if your script is not in the same folder as the executable you are trying to run. But in this case you would need to pass the full path to the file (not only the file name) in the first parameter.
So it's either:
RunWait, J:\Steam\SteamApps\common\Starbound\win32\launcher.exe, J:\Steam\SteamApps\common\Starbound\win32\
or just
RunWait, launcher.exe
if you want to pass a command line parameter, you just attach it to the first parameter with a space.
Like this:
RunWait, J:\Steam\SteamApps\common\Starbound\win32\launcher.exe pause, J:\Steam\SteamApps\common\Starbound\win32\
Sometimes the parameters need a - or a / in front of them. so it might also be /pause or -pause...