The first (and simplest) thing to try is disconnecting the Ethernet cable from the rear of the GoFlex and plugging it into the DNS-320 to rule out a cable/port issue. We know the port/cable combination work for the GoFlex. It's possible for a poor/damaged cable to cause data transfer issues.
The next thing you'll want to try is disabling as many of the services/apps as you can in the DNS-320 (e.g. iTunes, NFS, UPnP, AFP, etc). Cumulatively, enabling many apps that are processing at the same time can slow things down.
Also, as I suggested earlier, placing the DNS-320 and Boxee Box on a dedicated switch will isolate the network traffic and remove the router as a potential bottleneck/cause for your throughput issues. This approach will also provide a dedicated data pipe between the DNS-320 and Boxee Box, freeing up more bandwidth for the rest of your network.