The described problem is not limited to IE 10 and 11 (although it is not so discernible in other browsers) and can be demonstrated by adding the following CSS:

body {
    background-color: black;
    color: white;
}

When the reversed colors (a white text on a black background) are used, the flickering is present in all browsers and it can be reproduced with both CSS3 transitions and jQuery animations. As the browser's rendering engine should call its repaint method at some point after the animation has finished, the observed behavior is not connected with our controls.