I am no pro at this custom club/logo malarkey but did successfully manage to create a new team and get all custom kits and logos on, after much painstaking work haha. So some questions?...
1. Do you have two version's your loo i.e. a normal size one and a small size one? (I can't remember exact dimension of each one but if you know the dimensions of your logos please state them.)
2. Are they saved in separate folders, each with their own config file? (I added my logos to same folder as other logos and added appropriate line of code to that folders config).
3. Check your punctuation in your line of code in the config. I’m on MAC and it took me a few hours to realise that it had a habit of putting the “ marks in italic rather being straight, thus making the line of code “unreadable”.
It sounds like you have the config file and that set up since logo is showing so it’s most likely either the line of code itself or the image size of the small logo perhaps.