You should try a couple different things. First try stacking the item with z-index:
z-index: 1000000; /* max: 2147483647 */
Next, you can try and force hardware acceleration on your menu. The browser will create new rendering layers for your menu which may prevent the flicker.
-webkit-transform: translate3d(0, 0, 0);
-moz-transform: translate3d(0, 0, 0);
-ms-transform: translate3d(0, 0, 0);
transform: translate3d(0, 0, 0);
And finally, if your element is larger than the screen (even by one pixel in any direction), it can cause flickering during scrolling on some devices. Try adding the following:
-webkit-backface-visibility: hidden;
-moz-backface-visibility: hidden;
-ms-backface-visibility: hidden;
backface-visibility: hidden;