Flies see motion. When the monitor screen changes, the visible spectrum of the pixel is changing and nothing is moving.
Flies have limited color vision. Each color has its own wave frequency, but flies have only two kinds of color receptor cells. This means they have trouble distinguishing between colors, for instance discerning between yellow and white. Insects cannot see the color red, which is the lowest color frequency humans can see. However, houseflies have the ability to see polarized light, but humans cannot differentiate between polarized and unpolarized light. Polarized light is light in which the waves travel only in one plane. 
Monitors have polarized film on them so you could test the color hypothesis by taking an old monitor you are willing to sacrifice and removing the polarized film. Then you could test if the flies jump when the screen changes. See here for removing the polarized film on the monitor, or if you have access, this article on A behavioural study of polarization vision in the fly, Musca domestica may hold the answer without needing to ruining a monitor.