Failure to eject the clip on the Mac doesn't always cause the trouble fortunately, but it has for me once too. I also just reformatted on the PC in Vista and that solved it even without the firmware upgrade.
You would think the Mac would be smart enough to realize that it shouldn't be placing those invisible Mac files on PC formatted disks but it does. Oh well. So far it hasn't seemed to cause me any trouble. I have the kids use USB wall chargers since they have a good chance of forgetting to eject the volume.