To draw nuclei and electrons together, eFFview draws them on separate planes first, then renders them together as partially transparent objects. This sort of multipass rendering is still difficult to do in a fast way on modern graphics cards.
eFFview can switch between two methods, the accumulation buffer, which is slow but reliable; and framebuffer objects, which are faster, but are subject to glitches in many graphics drivers.
By default, the program uses framebuffer objects. If the program shows streaks or tears or crashes with a segmentation fault, try setting fast_frame_graphics to no, or equivalently use the flag /off, which reverts to using the accumulation buffer instead.
Some graphics drivers do not draw to the accumulation buffer properly. If the program displays nuclei only when using the accumulation buffer, try setting front_buffer_bug to yes.