Slitherine

If you duplicate a faction and use the duplicate in a second team, the commanders will only be available for the first team in the editor.
In the screenshot the commanders is only assignable to the blue Soviet faction.
In my case this means that this land commander is only available for the naval faction

Can't you just solve it by reassigning those? Like put the checkmarks for Soviet ground and Manchukuo to the 3rd human faction (1st in team 2, now blue), the Soviet naval to the last (now green)?

Then change the colors?

I have to admit I did not test it myself with that many factions, so don't overwrite your working scn, rather have an extra copy.