No matter how many konsole windows I open the environmental variables KONSOLE_DBUS_SESSION and KONSOLE_DBUS_WINDOW are always the same ("/Sessions/1" and "/Windows/1" respectively). It used to be that they were different for different konsole instances, though I can't remember the latest version in which it worked that way.
Testing here: KONSOLE_DBUS_SESSION is not always the same here, each tab and each window have a diferent session number, but KONSOLE_DBUS_WINDOW is always the same
How are you opening new windows? It seems to work here regardless of how "Run all Konsole windows in a single process" is checked. Note that I'm testing master.
This problem happens when I: 1) Right-click the screen's background to get a context menu and select "konsole" 2) Press Alt-F2 to get krunner and enter "konsole" 3) Enter "konsole &" at the bash prompt in an existing konsole window. However, if I have an existing konsole window focused and do "Ctrl-Shift-N" or select "File > New Window" from the menu THEN the environmental variables are set properly.