Whenever I push 'printscreen' or use the screenshot app I capture only my desktop background, see image:
Update
I tried shutter
as per Andrea's advice. But it does the same thing, only returns the desktop. However, it outputs some lines on the console that may mean something to someone:
org.freedesktop.DBus.Error.ServiceUnknown: The name org.freedesktop.compiz was not provided by any .service files
GLib-CRITICAL **: Source ID 1083 was not found when attempting to remove it at /usr/bin/shutter line 7249.
GLib-CRITICAL **: Source ID 1085 was not found when attempting to remove it at /usr/share/perl5/Shutter/App/ShutterNotification.pm line 186.
I use shutter:
you can then select: