The tick on application exclusions to work as inclusion instead is working the opposite way around - so when unticked it includes the apps and when ticked it excludes the apps.
Actually, I may have been wrong with my test as I received some clarification from the lead developer.
Can you detail what app and if you have the full path to the excluded app? Also, the app should be closed before it is excluded as there may be a small issue there.
Sean Drohan
Stardock Support Manager