abbad0n

When you say "opened the port" do you mean redirected the port (the one uTorrent is using) to the static IP address (or static lease through the DHCP) to the computer you're running torrents from? Also, which firmware (and version of the firmware) did you upgrade to? Also which model of Linksys are you talking about? Did you check if your computers firewall is what is causing the block? Basically, we need a lot more information before we can help you.

I'm not sure how you can have Torrent Options-»Maximum Number of Connections Per Torrent: 39.125

If your router allows changing the MTU on the WAN interface, how do you test for the best settings there? And how does it affect your computers MTU settings?