It's a strange issue that is know - Some USBs "reset" as if plugged in after the car starts, some have mentioned it's the actual chipset in the USB, other say it's the size or file system.
I had the same issue, changed the drive to a Sandisk 16GB and fixed the issue. Now it resumes the song that was playing and doesn't by default change to repeat/shuffle.
Thanks. My system resumes the stopped music OK where it left off. It just reverts to Repeat instead of staying on Shuffle. There's a few things I can check out tomorow that you have mentioned, but not tonight.