The issue in short:
Two obscure processing steps escaped unification: the fluid sieve from IF and AS grindstone put out the wrong nether quartz dust.
Additionally consider cleaning the dustQuartz and dustNetherQuartz of unobtainable dust variants to prevent JEI cycling through unsuable options.
Also in relation to the silicon issue, for some reason all recipes for all types of quartz dust smelting to silicon are visible wich makes 5 furnace recipe form wich 2 are actually usuable.