With the patch some new options were added to the adminpanel, and some old were hidden for some gamemodes, unfortunatly it wasnt done properly.
So if you look closely, when changing the Squad Size, the actual message is not changing the Squadsize, but the amount of bots for team 1.
I already sent a bugfix to fse, but if you dont want to wait for the next patch, download and use the new admintool version, this bug is fixed there aswell.
Another Workaround would be to close your game, restart it, and then join directly on the server already in CommanderBattle Mode. It should work then as long as you do not open the panel in another game mode, but no guarantee.