I think there's an issue with specifically crafting machines (not miners); I've got dozens of assembly machines with over a thousand crafts and not a single quality roll in my main base.
Running some tests in editor mode seems like this might have something to do with how (the hidden) beacons affect crafting machines and the update rate of beacons on assembling machines. Even with base quality set to 40 (150%) running an assembling machine 1 crafting gear wheels in the editor for 10 thousand crafts on very high game speed did not produce a single quality wheel, while a legendary assembling machine 1 is producing quite some quality wheels, but still a majority normal gear wheels (with more than 100% quality!).
I was considering making a bug report for this on the factorio forums but since it is a mod, it may be on the mod's end instead.
