He admonishes you for not picking sides, since that's all he knows or understands.
He's such a hypocrite. Doesn't like it when you don't pick sides, but pretty much hates all of them equally.
Yeah,he thinks Im with the freakin ncr even though Im with Mr.House.
That happened to me too. Fools based the dialogue off of rep instead of which quests you completed. <_< Here's a slight way to "correct" it, using another faulty "feature;" wear NCR armor every time you speak to him. That resets your NCR Rep to neutral, so he should get your allegiance correct then.