Hi there
I have a new DNS-320L and I am experiencing a similar problem. I have a single 3TB drive loaded and recently upgraded to the 1.03 firmware. I was initially seeing the unit getting stuck on 60% during the refresh, and thought it might have been a specific file so tried removing that file and re-starting. The DNS-320L then got "stuck" on another file.
I have since added more files to the drive (about 450GB in total) and now it gets stuck on 50%. It has a been sittting there for about 3 days now with no movement. It got to the 50% point within about 5 or 10 minutes, so I think there is a problem with the system.
I have also seen other people report similar problems with updating the iTunes database which leads me to suspect it is an issue with the firmware. I would expect to wait a while updating a database with 450GB of data, but not 3 days.
So, sorry, no solution for you, but you are not the only one. Hopefully someone from D-Link will read this and post a comment.
Regards.
sja