@wispie At first he didn't believe her because he was sure she was the enemy general and was trying to trick him...so it was right for him to be skeptical. Since her brother, the original general, was actually known to be quite short. If he easily believed her then he'd be too easy to fool.
When he found out she's not the real general, he did suspect very much that she might in fact be a guy, but then the princess's misunderstanding threw all that out the window.
So yea, he's not stupid. He was just being cautious.