SENTiNEL,
That is the correct displaying of the icons.
If you look in "C:\Program Files\Stardock\Object Desktop\IconPackager\Themes" folder, you will see all the Apogee folders.
The "Apogee" folder has the full set of icons in it.
The "Apogee (Amber)" - for instance - has the icons that will be changed when you apply that sub-package. As you will see, the "My Computer", "Recycle Bin (full and empty)", "Hard Drive (normal, and network on/offline)", and folders are the only icons that change when you apply the Amber sub-package.
This holds true for all the color sub-packages, so when you apply a sub-package, IconPackager exchanges the icons found in the sub-package folder for the relevant icons found in the main "Apogee" folder - and then applies the exchanged colors and the balance of the main "Apogee" folder icons.
I believe Mormegil is going to update the pack to add some file icons to the main pack, as well as add some format sizes, but since we have not seen this yet - I am not sure on that one.
I hope this clears up the question for you.