I've had that happen, SH3 commander goes through the motions of launching SH3 but, SH3 does not launch. When this does happen, if you go ahead and launch SH3 from its own icon, it works as if it was launched by SH3 commander right up until shutdown. SH3 will shutdown but, SH3 Commander is still running as a background process, and you have to kill it through the task manager. Then restart SH3 Commander to do the rollback. It is a pain but, it does work. I'm not sure how to fix it, as mine started working correctly again one day.
