You have most likely overwritten /overridden the xml file that comes with the game.
If you have put the images in the game directory (C

Program Files\etc...) rather than the user data directory (My Documents\Sports Interactive\Football Manager 2007\etc) then you have overwritten the config file that is needed for these images.
If you put it in the user data directory and used the same directory structure as the main game does, then it could be using this new xml file instead of the game one. The solution is to put this in a new sub directory, so that it's something like this graphics/pictures/logos/my logos/...