On 1.16.5 using 1.0.3.0. I have a Tier V factory with lvl 3 Perks and 3 controllers. I can see the progress bar going to 100% and no loot is produced. Sometimes after 10-12 cycles it will produce loot and goes back to nothing for a few cycles. I have an Ultimate Conatus cell so it has enough as it requires 10752 mB. I can see it using the Conatus fluid every cycle though.

Some mods need ingredients provided in a chest beside the importer.
Are you providing the correct amount of wither skulls and soul sand?

Yeah, I thought all the other mobs would spawn if the withers had no ingredients. Since then I have a constant flow of skulls and soul sand coming so the issue is gone. Thanks Ipsis.