| Those that were unchecked reverted back to original Windows icons. |
This is the correct behavior in my experience.
If you go to View > Package Builder, you will see all the icons that IconPackager can change - and which default icon represents each.
When you deselect some of the check boxes in the Package dialog to only apply certain icons, it applies in the same way it would had you drag-n-dropped the specific icons into Package Builder and left the others in place (which of course are the default icons).
If you want to modify a current theme, you would apply the theme completely > click the "Icons and Cursors" category in IconPackager > change the icons you want > save the package.
If you want to create your own theme with some icons from other packages, you can use Package Builder to create the package. Note - the drag-n-drop method requires individual icons, so you would use IconDeveloper to open an icon library (".icl" file) and extract individual icons to a folder. Once you have all the individual icons you want for the theme in the folder, you can drag-n-drop into Package Builder to create your theme, and then save the package as a unique name.
Note - I have found that going to the saved theme (after saving) and double-clicking to install and invoke IconPackager, removes any possible issue with not being displayed or accessed in the Package list after creating.
BTW - I tested the functionality of version 3.00b.093 to apply themes partially on both a laptop and desktop, and all worked perfectly.
One item of note - if you have one or more of the "Desktop, Start, Folders, Drives, or Others" not checked - you receive this message after clicking "Load":
If you happened to select Yes, and then place a check in the "Do not show this message again" box, then you may have issues trying to apply partial packages.
If you do not see this message when loading a package as indicated above, and you want to reset this notification, you will need to go into the registry (unless you want to reinstall) and change the "Notice Apply" data value back to "1" in the following keys:
HKEY_CURRENT_USER\Software\Stardock\IconPackager
HKEY_USERS\S-1-5-21-776561741-492894223-682003330-1004\Software\Stardock\IconPackager
Note - changing the first key listed should reset the second one listed, but check to be sure. If you are not comfortable in the registry, then reinstall would be an option to reset the message - which allows the user a choice each time. 
