Weird, it should change. It's possible the color change doesn't stick when you do it after you start a game but it's fairly easy to change it in the save file. Just make an uncompressed save, autosaves are good for that, use Notepad++ and search for the old colors and then replace them with the new ones.
As for the flag, be sure to check you don't have multiple mods affecting the same title. I don't have the latest version HIP installed now so I can't check their files out.