What version of AdminStudio are you using? In 5.5, Repackager (isrepackager.exe) reads one exclusion list, which is a minimal list. When opening up IRP with ISLC.exe, ISLC.exe reads isrepackager.ini to apply default exlusions on differences captured by Repackager. From ISLC.exe, you have the option to apply different exclusion list by using different INI file. If my memory serves, this behavior is in AdminStudio since 5.0.