At least on my system (Gnome, metacity window manager) some (all?) pop-up dialogs are modal (not sure this is the right descriptions), i.e. I cannot interact with the main window while they are open. This is a big problem in some cases (see bugs #445 and #447).

Interestingly, the radiation spectrum window is *not* modal, probably because it is not really a dialog and does not have the usual "Close" button, but is only closeable via the window manager close icon.