Thanks to ernieschwitz for alerting me. Sorry, I didn't check the site today.
The instructions are:
1. Install it like any other scenario file or mod with the "Install/Zip" button. This will create the directories
in the graphics directory. Inside these directories is a directory "natocounters" where the files are.
2. You have two choices. The first option is to use the editor for whatever scenario you want to use them with (if you change the Anewdawn masterfile, random games will use these systemgraphics). In the editor, click the "Setng" button, and then you will see a blue button on the left side with a left arrow "<-" that says "System Gfx Overrule". Click this button, and you will be prompted to enter the directory name inside the graphics directory. This would be Nato-systemgraphics. This will then use these system graphics instead of the default. The second option, is to rename, or copy these, into directories just names systemgraphics (BIG and SMALL as well). But, you should save the originals. Either way, be forewarned that if there is an official patch, these would likely be overwritten, and you'll have to do it again. A similar thing is true for the BIG German flag 5.png and 5b.png (the default is corrupted).
I just downloaded it an installed it myself, so I had no trouble with the files, and they are fine. So, I am not sure why it would take a minute to install. That is quite odd.
You will need 228b or higher in order to use them. Otherwise it will only use the first 64 or so graphics files. It will probably display them, but if you try to set them, you will get a CTD with a subscript out of range.
The other thing is that if you make a template, the template will only save the first two graphics, so if you use graphics 3 and 4, you will have to reset these with each new game (not my fault).