I'm sorry but, other than DX10 mode (which the scenery doens't support), I can't think of any reason why the buildings would disappear at night/dusk only.
Something like this might happen if you lost all the night textures, since in FSX an object that can't find its textures, sometimes disappear, but it shouldn't normally happen, and it should be cured with a reinstall in any case.
Have you tried other sceneries we have ?