Maighstir: After the mount commands should be the name (perhaps with path, as seen from inside DOSBox) of the application you want to run, exit should be after that (as the very last autorun command).
If that's already the case, sorry, it wasn't clear from the information given so I'm just making sure.
jjsimp: I'll have to try that. I don't have the launch command in the config file. I have the launch command in the target field of the shortcut I run:
C:\DOSbox\DOSBox.exe -conf "c:\DOSbox\AOR.conf" "C:\DOSBox\Games\AgeofRifles\Rifles.exe"
Then try adding -exit at the end of that command line, that should work as well. You can have either both in the config's autorun, or both on the command line. Since the commandline launch is run after the config's autorun, your "exit" after the mount commands ran before it even tried to launch Rifles.exe.
EDIT: Assuming you mount C:\DOSBox\Games\AgeofRifles as DOSBox's C:, the command in autorun would be C:\Rifles.exe