Menu bar icons flash when changing Desktops

When switching between two Desktop screens or Full Screen apps, some of the icons in the menu bar flash because they redraw themselves, causing a jittery, flashing effect. This started happening after upgrading to Yosemite. I have an external Thunderbolt Display attached to my Retina MacBook Pro (2013) and have separate Spaces activated. This is specially visible when the Dark Mode is enabled.

From elsewhere:

It seems that, at least in the case that I'm experiencing, the specific description of the problem is that: When at least one external monitor is attached, and the built-in monitor is also in use, and Displays have separate Spaces is enabled, one can click the desktop on the inactive desktop (the desktop with a grayed-out or muted menubar), and that menubar's icons will begin redrawing, which manifests as a jittering of icons, a rearranging of icons (in the case where one has rearranged them manually by holding down the CMD key and dragging them), and a brief de-antialiasing followed by a re-antialiasing (or dithering) of the icons. This occurs with all icons in the right-hand side of the menubar, but not those on the left (apple, and menu items), and also excluding the sidebar icon. The symptoms do not occur when transitioning from one external monitor to another.

As a last resort workaround, you can disable Displays have separate Spaces in System Preferences > Mission Control. Though this will remove the menubar from your ancillary displays, and also (obviously) the separate spaces functionality.