It turns out that my issue was due to a bug in two other mods and not this one. The way the quality condenser changes its base quality with research, is that the mod makes an invisible beacon which applies an added quality effect to the condenser. That's why this mod has "beacon interface" as a dependency.
However I also used the Voidcraft mod, which had some code which unintentionally made the beacon interface ignore its own modules. The Voidcraft dev fixed their bug, but it's possible you have some other mod which is doing something similar and breaking the beacon interface.