I use Beacon Rebalance by wretlaw120 and while the productivity modules work in the beacons the quality ones do not for me. Not sure if its a compatibility issue or what. Anyone have any ideas? I tried the mod settings and dug through the lua files in the mod to see if there was a setting that could be overriding things but i didn't see one. I might just have missed it. Any help to get this working would be appreciated.

Had a similar issue, but for me, i just had to go through all mods very carefully and find those that altered modules or beacons.
Here's a list of some mods that can prevent quality modules from being allowed in beacons:

More Module Slots, Terrawind Beacons 2, Bob's modules, Unlimited Productivity 2.0 compat fork (and presumably the original version as well).
If you have any of these other mods installed, or any other module-adding / beacon-adding, etc...check those closely.