As a temporary fix on Windows 8 until they fix their product, I figured this out.
Replace [USERNAME] with the username you're using. Delete everything in that directory. This is the icon cache for Windows Explorer. After you do that, reapply the theme in IconPackager.
Stardock: As this issue has been going on for some time apparently, please fix your product. On startup, IconPackager should delete the cache in the directory above and delete everything in that directory when you tell it to delete the icon cache. It's a simple fix and as its more a Windows Explorer issue as its hard wired into it to cache the icons, this might be the only way to make the icons stay themed. People can turn off icon caching in Explorer, but I don't think it will help. I haven't tried it yet, though.