Comment 2 for bug 1005531

Thanks for your bug report and helping to makle Ubuntu better.

You have the option in empathy to edit which port is used first.

In the account wizard, click the IRC connection you want to change
Click to Edit Connection Parameters
Click "Freenode" (Thats the Ubuntu server)
Click edit when freenode is selected in the server list
Expand the window down, and select the freenode listing with 8001 as the port, then using the up arrow click it until it does grey and you've made 8001 the default server port that empathy will use.

Although, That's too many steps and quite confusing for the average user. Marking this as a wishlist bug and hopefully the upstream devs will follow quit (if you can't).