You've already answered your own question. In your second screenshot you can see the icon type: "Tool". I've highlighted it for you. Def_icons need to be "project" type icons, to which you assign a default tool. See the additional screenshot from my system.
Did you use some kind of installer utility to copy these icons? If so, it might've mucked them up. It might be possible to open each one in IconEdit and change them back from Tools to Projects. There may also be some utilities that allow you to do this en masse. My suggestion would be to just re-download the entire archive from Aminet and copy them overtop of what you have currently. That's probably going to be easier/faster.
Off topic, but, Mike, what are you using to change the looks of the window borders, as well as the menu bar at top of the workbench screen?
