I'm not sure the exact name of this crisis. I think it might be cylon detector sabotage or some such. Anyway, if you fail the crisis, no players can look at someone elses loyalty cards. Furthermore, the card states that it remains in effect. The question I have is does this card then negate Baltar's once per game ability to look at loyalty cards or does it only apply to other situations in which a player could look at loyalty cards. My game group house ruled it as allowing Baltar to still use his ability, but I'd like an official clarification if there is one. Thanks.

Yes, this does negate Baltar's once per game ability.

I hope that this answers your question!

Wow, I thought I might have trouble getting my players to follow any ruleing that the crisis applied to Baltar's ability, but I don't think they can argue with me when I show them that the game designer says it's so. Thanks for the prompt answer and thanks for creating another great game.

Even if Corey hadn't posted -  why would they argue against logic? The card explicitly says "players may not look under other players' loyalty cards" and stays in the game.