If you're using an actual HDD there might be a power issue as spinning the disks takes a lot of energy. Try using a flash memory drive instead. I've got around 16 gigs on a 32GB drive and it works perfectly, finds all of the tracks pretty quick.
Also the file format could be an issue. I know the car supports MP3's but if you load .wav, .flac, .acc, etc then it just might not support those files altogether (I don't have the full list of supported formats so check your manual/dealer
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