Heh, you get what you ask for. Don't have much time now, but I did run that fragfile tool on a 3 GB file that was transferring slow for me. Here was the result:
200519 extents found, perfection would be 25 extents.
That file only transfers at like 8-9 MB/s. Now, here's an 700 MB iso that transfers at 25-30 MB/s:
15 extents found, perfection would be 6 extents.
So I think it just might be possible that fragmentation is an issue on the DNS-323, and will affect transfer speeds.