Hmmm... No, that is a bit strange. I would suspect a disk error or memory error at that point. Does it only happen in the car, or will it also happen on AC power. If it does happen on AC power, try to capture any error messages with hyperterm.

The only issues I have seen with lots of files are that the temporary storage partition and playlists are a bit strange / can get too big.

What version of the player, software, etc.? Can you also turn on the disk access icon, so you can see if the disk is spun down or if the audio thread is waiting for data?