I just tried replace two icons and save it. Applied and it work for me. Here my steps.
1) Set icon packager to use Windows Default Icons.
2) Click Customize -> Click Package Builder -> Click and drag my old Documents icon into "Documents". And than click my old Computer icons into "Computer" -> Click save -> Saved -> Go back to "Look & Feel" -> And my new saved icon pack is listed there. Click on it and applied and it work. Both Documents and Computer Icon change accordingly.
Try it, just try to change those 2 icons and see it work for you. If it still don't. Maybe uninstall and reinstall could help. Follow below steps.
Please try uninstall and reinstall Iconpackager. But, just to be sure, follow this steps.
1) Apply MS official icons via iconpackager. Reboot.
2) Uninstall Iconpackager. Reboot.
3) Make sure all icons is back to their Official Microsoft Icons set.
4) Reinstall Iconpackager. Reboot.
Try changing those two icons again.
Stardock Community Assistant.