Example.. I go to groups click on (drive icons) I get folder icons
click on folder icons I get other icons.. click on drive icons again I get drive icons click on desktop icons I get drive icons. The list is always changing. Same thing happens when I choose show in groups the list is always different.
That menu list is to toggle on and off which groups you want to show, IMO it should have check marks to show what is selected but it does not. Click them as needed until you have all groups showing in Package builder then do not touch it again.
I have downloaded again, after making sure all from before deleted, unzipped, renamed IP to zip, unzipped, here is what is in folder ( not installed so no IconPackager interference on my end ), I see at least 6 icons from your preview pic that are not in folder