You're no longer able to select scout and select the entire planet to globally search. Why is that? So much micro.
I just tested it out as well in the current stable build and it works fine for me as well. So I click the scout, then click the patrol button in the menu on the right and then drag a circle over the entire planet and off it goes. Can you two try again while starting PA with --nomods to rule out any pesky mods interfering with the patrol command?
By the way, is it possible to let a orbital scout jump to each planet iteratively? Such as using area patrol to cover multiple planets. So the players can really scout the entire system globally.
You can give move orders sequentially like that, but not patrol orders. A unit will follow along it's list of orders faithfully until it reaches a patrol order, and then it will do that single order forever.