In your original site, did you have the files stored in the database and the file system or just one or the other?  
What's happening is:  
- you exported just the media file database records and not the physical files  
 
- on your import you checked to import the physical files, however, during your export you never exported any
 
- you manually copied files from one server to another
 
- your new database (site you imported to), has a database record but no phyical file OR there is a physical file but no database record.
 
- OR worse yet, a ghost database record which will cause a collision when you try to import that file with the same name.  
 
My suggestion would be:
- delete all those logos from Kentico using the Media Library UI.
 
- Delete any physical files from the file system from that logo folder
 
- Query the 
Media_File database table looking for a library ID and/or a folder path that matches the location of the logos.  Something like select * from media_file where filepath like 'logos/% 
- Review any of those records and manually delete any necessary from the database.
 
- Export the media library files again AND the physical files.
 
- Import the media library files and the physical files.
 
The other option is to do the following:
- Manually copy the files from one location to the other
 
- In the Media library, perform a mass import
 
- You can mass import by selecting all the files necessary to import, 
 
- Click the Import button,
 
- Check the box to use the same description for all 
 
- Uncheck the box to show a preview
 
This will import all the images in a short amount of time to the database.