Yes - I think you've ID'd the cause... I AM almost exclusively playing random scenarios...and that's where the custom army option has vanished... but I don't understand the reasoning for the change... EVERY game has a deployment phase... even when I don't change out units I still usually move/rearra...

I've been playing the game for quite some time and suddenly last week the Custom Army option disappeared from the new game setup Option menu... the button is flat gone from the menu! I'm running the Steam version and checking the local files properties I'm told they are correctly installed. I wonder...