I never had a problem getting my HD icons to work, that's weird
It's mostly because I use photoshop and the Nvidia .dds plugin. Paint.net (assuming you use that) doesn't have nearly the same troubles, but it also has far less options.
I started over from scratch on the file containing the icons of trouble, just to make sure I didn't goof anything. It *should* work, but if it doesn't, I'll use the other saving style. (smaller file size, but the colors kinda get dulled.) The updated file is in the main post.
One thing I'd like to note, as I started over from scratch on that file, I also used different tools and whatnot, and it might look a little different. I do intend to remake the others as well, but let me know how you like the changes. I've kinda stopped going for a 100% remake of the original HD mod, and started using my own methods and shooting for what looks good. (Besides, Topaz Vivacity is a dilapidated program that isn't compatible with my version of Photoshop)
I hope it fixes your issue. NovaDragon. When I finish recreating the other icon files using this new style (assuming it's well received) I'll be uploading .pack versions.
Geeky footnote: The file in question looks like the below. Either in my edits, or through the saving I used, the black where the number icons are become something not black, so that instead of being a transparent overlay, they became a black veil over the normal icons. I wonder why nexon chose to use it as an overlay instead of just on the icon itself...