I think it might be something to do with your margins having different values as your screen width reduces in size. as it switches from one media size to another, you'll probably find that the percentage of margin switches from a smaller value to a larger value.
Basically, at 481px, your left margin might be 10%, but at 480px, your left margin might be 15%. Even though you have changed by only one pixel which might equate to 0.5%, the media query is pushing your logo away from the left margin by an extra 5%.
Does that make sense?
Anyway, I like your menu and how it disappears to a single button… where did you get that from?