I wanted to start by saying that System Builder is for when the controller has lost its OS (Baseware) or you want to install a new system on a controller that has a OS already. So has the controller lost it's OS?
Anyway, when you are in the System Builder and you click on a System that you want to install on a controller and you get that error, it normally means that the BaseWare version you are trying to use is missing. So in that XML file that you opened what version does it say you are trying to use? If you go to C:\Program Files (x86)\ABB Industrial IT\Robotics IT\MediaPool do you see a folder with that version? Like "RobotWare_5.15.0266" if the version you are trying to install is 5.15.0266. You may need to install that version of Baseware before you can use System Builder to download the system.
If you are connected to the controller that you want to download your program changes, then you need to connect to the controller through the Controller Tab and then get write access and load your program changes directly into the controller.
Hope that helps