I doubt that there is any connection to purchasing music from the iTunes Store, because those are just regular AAC 256 kbps audio files.
What you describe could be caused by the hard drive in the iPod becoming unreliable. It may also be a problem with the connection between the iPod and computer.
Try shutting down the computer and disconnecting all USB devices, including any hubs. Start up with only standard keyboard and mouse connected (if normally used).
Run iTunes and connect iPod to a direct USB port. If necessary, do a Reset on the iPod (while connected)
Try doing a Restore again.