yeah - If I understand correctly you are unable to select the extra spell for anything other than '0' level spells? I had this problem too and was a little tricky to work it out.
If this is the correct 'problem' you have to go to the tab 'in-play', and under the heading 'Activated Abilities' select the spell level you want the favoured class option to apply to.
hope this helps
jaynay27