Linux is going away from the geeky side of computing quite quickly, some of the most computer illiterate people I know use it with no major issues.
By default Ubuntu locks down all ports and services, so that your computers pretty safe from the outside world. This may be whats causing your headaches here, try running the following command to open the ports in the firewall:
sudo /sbin/iptables -I INPUT -p PROTOCOL --dport PORT -j ACCEPT
Replace PROTOCOL with either tcp/ip, and replace PORT with the port number you want to open up.
Just reread your original post, if you have already tried this then I can only offer two more ideas.
a. Make sure that the ports are being forwarded through your router, and that they are being forwarded to the correct computer (see http://www.portforward.com
for a lot more information.
b. Your ISP is attempting to block P2P downloading - either change the ports you are using to connect, or change your ISP.