The colour of the missing letters is decided by the first colour in the pallette. As long as you don't select that as transparent, it shouldn't be. But that wouldn't really explain why the command window letters or the location window letters show up, unless Yanfly didn't set them to normal_color when he made them.
My best guess is that you made White a transparent colour when you imported them, and that's why it showed up like that. So don't do that. If you need to, you can just make the part you want to make transparent a different colour in Paint, and then select that as the transparent colour.