Ummmm...What version of dolphin is this?
like 1.2, 1.3, ...
it is version SVN 1546
the most up to date version is SVN 3095
so your version is from last year i think
Cripes! Must get new version then!
EDIT: Hmmmm... Controller 2 does not seem to work on the newest version. Know why?
It works fine for me. What plugin are you using? What have you done to try to configure it?
Updating from an ancient rev?
Go to General Config, under Gamecube tab, switch Port 2 to "Standard Controller"