It absolutely doesn't invalidate you as a female (and you're definitely not the only person who feels that way, either - sometimes or all of the time).
I think you've mentioned before that you've read our Trans Summer School series, but your post reminded me of the
"Am I Trans Enough?" section in particular, especially this line: "Everyone defines and relates to gender in their own way, and there’s no wrong way to gender." That includes not just how you express or identify your gender, but how strongly you feel about it. For some folks, their gender identity is a very significant and important part of who they are, and something they feel really consistently strongly about, but for other folks - sometimes or always - it just isn't that important or something they spend a lot of time thinking about. Everyone relates to their gender differently, but that doesn't mean that anyone's femininity (or masculinity, or genderqueer-ness, or agender-ness) is invalid or wrong.