I have been replaying with the initial save at the end of turn zero.
Those are two different files, only one of which has Initial as part of the file name. Both files have the terrain and civs set. My unsubstantiated theory is that is the one with Initial as part of the file name has not set the +/- values for bias.
Is there any way to figure out what random upgrade his units are getting?
From one of your ranged units, you can see the promotions after targeting but before firing, and not just as part of the odds calculation as you will also see his unit icons. Otherwise, I think selecting AI units is problematic. My observation is that the AIs especially favor medic and cover, but Shaka probably does not fit this pattern.