Are these music tracks that you have bought through iTunes, or ones you have ripped from a CD within iTunes? If you have ripped them, it might be worth checking your rip settings in preferences, i had mine set to AAC Encoder - iTunes Plus and i never had a problem. I recently converted them back to MP3 tho as i found some devices wouldn't play them atall, was never an issue with the car though. As a test, you could try converting one file to the iTuens Plus format in iTunes. This can be done by changing the Import Settings in preferences, then find the file in your library within iTunes, then right click and choose (in this case) create AAC version (i think). You can then try converting it to an MP3, by again changing the import settings and right clicking (this time it will say create MP3 version).
I would create one of each type, change the names accordingly and see how they perform?
Im not familiar atall with the business nav, although i wonder whether these other files could be album art/info that the nav should be picking up? I never had this problem with my Golf MK6 either (just seen your note about the Audi)
On a side note, are you individually copying each file to the root of the USB? As the iDrive system will cope with your files in folders
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