I tried a few times and I cannot reproduce your issue on my setup, I have the same downlink and uplink on 2.6.2.1 and 3.0.1-RC9. I can suggest you try to start Wireless Link Test a few times (for example 3 in series) than change firmware and make same tests on it. If you want, you can upload or send on my mail (mykola.rudenko@cambiumnetworks.com) your configuration files from AP and SM, and I will try reproduced it again on my setup (maybe root cause in some specific configuration on your devices).
I tried to start Wireless Link Test more than 10 times always with the same result. Changing the firmware results in a throughput decrease if I upgrade from 2.6.2.1 to 3.0, and throughput increase If I downgrade from 3.0 to 2.6.2.1.
Based on your screen shots, it seems pretty clear that v 2.6 is selecting MCS-15 and v3 is preferring MCS-12 for some reason. It would seem like the algorithm is maybe now erring on the side of caution?