based on what you wrote i think you expect the gestalt tab dropdown to give you a list of all classes. That is not how it works. The dropdown list classes that have been added to your character.
If i was making a fighter/rogue
1) on the "classes" tab you add a level of gestalt.
2) on the "classes" tab add a level of fighter.
3) on the "classes" tab add a level of rogue.
4) switch to the gestalt tab and select fighter from the first dropdown and rogue from the second dropdown.
thank you so much!!!!