Thanks for the report. It really helps if people post their problems. It seems like I saw this issue once, but thought it was just a fluke since I've never seen it again. What checkboxes are you talking about exactly? For Gnome and KDE?
As far as the XFCE menu button goes, that should be easy to fix. I believe you right-click on the menu and then "add applet"? You should find the menu button in that.
Jack server is really easy to fix. I am pretty sure the manual addresses the issue you describe. All you need to do is open QJackCtl from the Multimedia menu. Then, click on "options" or "configure", whichever it is, and deselect the checkbox for Realtime. Then, close the configuration dialog and you click the green start button which will fire up jack. Then, any program that needs it will plug into the running jack server.