@Captain_wiggles you are my hero. That did work. So it was the beacons decreasing the quality.

I have Tier 1 Quality Modules installed in an Assembling Machine 3 that has never produced even one uncommon or higher quality item as an output. It has been running for a week a straight and dumping directly into multiple chests so that it was always running and filtering out quality items, but ...

There are mods that do this already like "Rate Calculator" and "Max Rate Calculator". This is an essential part of the game being able to calculate the real rates based on your current modules, number of beacons, research speedups. I wish this was in vanilla, its the only thing keeping me on modded ...