After selecting Rogue, you gain a prompt to select a "secondary class," but are given no further information on what exactly that means. You are able to choose from any base class from the Player's Handbook (except Rogue, of course), the Expanded Psionics Handbook, or Complete Adventurer.
You are also given the option to apply your Moderate Boon to this choice, though the button seems to have faded away almost completely.