I just upgraded from 3.3.16 to 4.0.3, but nothing was going through. All torrents were stalled and no traffic was passing. Took me awhile to figure it out, but I finally discovered that during the upgrade, the Proxy Server type changed.
I had it set to SOCKS5, but somehow during the upgrade it got reset to HTTP. Switched it back to SOCKS5 and all is good now.
Hope this helps someone else.