When an application opens a new "pop up" window, it doesn't show in the Task Manager or Task Switcher. If focus is lost from the window, the only way to get to it would be to minimize every other window or close and open it again from the main app window. It's hard to define what constitutes "pop up", but here are some examples:

in KTorrent: File > New or Settings > Configure KTorrent or any other new window opened in KTorrent
in Ardour: Window > Key Bindings
but opening Window > Mixer in Ardour DOES treat it like an existing window and it shows in both the Task Manager and Task Switcher.

New instances of any program also do show up. It seems that just the small windows are not getting picked up by as tasks?

I'm using KXStudio 14.04 with KDE 4.13.3

Either non-modal transients (but they're not skipped by the tabbox, ie. alt+tab):
http://kde-look.org/content/show.php/Un ... ent=161366

or a utility window:
run "kcmshell5 kwinoptions" and in the "Advanced" tab untick "Hide utility window for inactive applications" (hint: if you're still on KDE 4, it's probably not "kcmshell*5*"