When you formatted your drive, were there any bad sectors? If that is the case, then that would explain your problem. If not, then try checking the disk for bad sectors. This would be done by going into My Computer and selecting properties from the
right click menu. Then, go to the tools tab and select check now. Select all options and start the check. If there are no indicated problems still, I would recommend just zipping your files and placing them on the flash drive and transferring them that way.