Unforunately, in the process of using IconPackager, all the icons in my Start menu have been messed up.  Now thankfully I found a workaround (applying the icons from the Quest theme and then restoring Windows defaults appears to have worked) but at the same time I'm concerned.  I'd really like to see an option to exclude an icon from a theme's change if there is none there.  So if there's no changed icon for a .exe (and even there, custom icons shouldn't be affected) no change is made there.

Pease consider adding this option to a future update of IconPackager.