When you use the Extrude command the software makes a "best guess" at whether you want to Join/Cut/Intersect/New Body/New Component.
If you select what you want to do in the dialog box before you extrude it ignores your request and goes back to the "best guess" method when you start extruding.
Could the software be configured so that if you've selected the type of operation before you extrude that it recognises that you know what you want to do and stays with that selection once you start extruding?
A minor irritation in what's a great piece of software.
Best regards, Steve Cox