Disclaimer: I haven't used the jumbo frame feature on the DNS-323, so I'm just replying in a generic sense.
When you enable jumbo frames, you are essentially modifying the MTU. When your browser communicates with the DNS-323 web server, the client and the server must negotiate a sensible MTU. Mismatches are usually communicated (and then resolved) via ICMP messages. However, the web server may be blocking ICMP messages, meaning that a proper MTU can never be negotiated.
Now when you transfer files, you are using Samba, which has nothing to do with the web server.
So my guess is that somebody is dropping ICMP messages along the way... Very wild guess though.