Is it possible to have an option that would warn the user that MCEBuddy is converting or scanning for commercials, when they try to shutdown the system? Obviously this is difficult, as Windows would likely think MCEBuddy is a nonresponding program and end the task anyway.
If this isnt possible, I think another idea would be a small window that sits in the desktop (possible a Sidebar Gadget?) which indicates if, and how long, MCEBuddy will take.