I have a similar problem as described above. I have tried customising some individual icon selections, changing from the default to something else, then reselecting the original, but to no effect.
I downloaded the latest IconPackager to test it, on an up-to-date Win 10, and applied the ootb Flash Live icon set. But only some of the icons applied as they should. (This was with a clean, first-time install, and the same after uninstalling and reinstalling.) Specifically, in Explorer, in the navigation pane, only the Computer and Network icons updated. None of the other quick-access icons changed from the defaults. And within the file listing, none of the icons reflected the theme - for the screenshot, I added an empty folder and Word document alongside the txt files.

I did attempt to download an icon set from WinCustomize, but that was no better.
The only setting I have configured that might affect how icons work is shown in the above image: image files show thumbnails of the image itself, rather than a meaningless file-type icon.
Any suggestions to fix this appreciated, as I would like to buy the product and reskin my icons…