When I pulverise ores (only testet with iron_ore) the primary output is deleted (iron dust ore what the name is). Only the secondary output comes out with the normal chance. (I have a iron furnace under the pulveriser and have auto pull and push enabled in both machines)

Tested with just the pulverizer and this works fine. Could be a bug related to having both of them pushing and pulling - try having just the pulverizer pushing into the furnace