Im looking to see if it showing the wrong information when it adds the file to the UPnP AV media server index on the fly as opposed to a manual refresh since he stated his original files he was having an issue with now show the proper file size. There was a similar issue with the UPnP AV media server on the DNS-323 with files larger then 2GB, however it did not correct itself over time and show the proper file size. this issue was fix in the latest firmware.
hOOch, Something you can try if you dont mind. Factory reset the DNS-321 when log in and run the manual refresh and see if it immediately fixes the issue with all your file. That may give us a better idea of what might be going on.