Hey Mike, So to understand how the clear logos and banners work you need to know the way the files work also where LaunchBox first adds a new systems Clear Logo and Banner so.....
First the scraped Clearlogos and Banners etc. go to ----> C:\Users\........\LaunchBox\Images\Platforms\Arcade(or what ever platform)\Clear Logo. or Banners... and these will be the standard ones used in BigBox, So you shouldn't really change them here.
Now there is a theme called Default and in there is a folder ----> C:\Users\.......\LaunchBox\Themes\Default\Images\Platforms\Clear Logo. or Banners... but inside the folders they are empty (apart from a ReadMe file), again you shouldn't really add them here as that will make them the new standard logos / banners.
So in a newly downloaded theme or a copy of the default theme to make your own theme, you can add your new Clear Logos / Banners in there ----> C:\Users\......\LaunchBox\Themes\(your new theme name)\Images\Platforms\Clear Logo. or Banners....
Hope this makes sense I know its a long winded reply but I'm not sure where you have been adding your logos / banners so thought it best to explain first. So if you check your folders in that order you should be able to see which ones are getting used. ohh and Don't forget to Refresh the image cache everytime you want to use new Clear Logos.... Options---->Image Cache---->Refresh Platform Wheel Cache