Check out whether System Settings/Window Behavior/Advanced/Placement is out-smarting you ;)
BTW, maybe unrelated to the issue at hand, unset "Hide utility windows for inactive applications" if you think that other QjackCtl/Setup/Misc/"Keep child windows always on top" may help in the process if turned on.
Same here (kwin 4.4.3).
Check out whether System Settings/Window Behavior/Advanced/Placement is out-smarting you ;)
BTW, maybe unrelated to the issue at hand, unset "Hide utility windows for inactive applications" if you think that other QjackCtl/Setup/Misc/"Keep child windows always on top" may help in the process if turned on.
Seeya