In an EM plant with 3 rare quality modules and 2 uncommon ones, out of 36 crafts, I've only gotten 2 uncommon modules. While it's a small dataset, this is a measly 5.6% chance for uncommon on a machine that states it should be 18.6%. It's possible this is being caused by an incompatibility within my modpack, but I haven't been able to pin it down if it is, and the quality number on the machine's effects is in line with the intended value.

Testing in editor mode does average out to expected values; however, across nearly 300 modules crafted in my normal save, the percentages are far lower than expected. Somehow, the save itself seems to be broken? Or perhaps it's just cursed and 1/10,000s unlucky.

Did you check for a nearby beacon? Speed modules have a negative quality modifier, and may kill any benefits from quality modules in your assembler. Tested in same conditions as you describe (EM plant, 3xlvl2 rare, 3xlvl2 uncommon qual modules) and I average out at 35ish% as expected.