Anath
Since there is a few events/plots that work only if all the cards you have match your house affiliation, so I was wondering. If I go treaty on say.. uhm.. Stark / lannister and choose Stark as house card. Does Lannister characterss/cards sitll count as within my house affilitation?

Similiar, does in-house count as both your houses on a treaty?

ktom
No. On Treaty, only the main House (the main House card you put down, not the one you name for the Agenda) counts as your "House." It's the same reason you can only play "House X only" cards for the main House (not the one you name for the Agenda) with the Treaty Agenda.