Regarding to your problems, I think you need to check two things:
1. How many GB can your car stereo support?
2. What is the format of the other songs that can not be played? Is it not a format supported by the car stereo?
I have a Kenwood KDC-MP435U car stereo that has a USB port. After spending several days copying music to an 8GB thumb drive, the car stereo only plays about 100 of over 1700 songs. Anyone know why? Can it only read 100 or so? And it always plays the same 100. Using the remote for it, I've tried to punch in song number such and such (one that's way past 100) and it just goes back to the song it's currently reading. I've read the manual that came with the stereo and also Kenwood's online manual as well but nothing about how many songs a thumb drive will play. Any help at all is very appreciated!! Thanks in advance!