1. Opened the program.
2. Click backup.
3. Select all colors I want and hit install.
4. Closed the program.
5. Went into game to check if it worked. (And it did).
6. Closed the game.
7. Opened the program again.
8. Clicked restore. (It said it successfully restored).
9. Went into game to check if it restored. (Which it didn't enemies are still red. Allies are fine though).
I'm not a noob at this.
EDIT: Never mind, I fixed it, had to do it through verifying the files.
You might want to take a look at that "bug" though..