The following images represent the evolution of the NewsWatcher Preference's dialog over a number of months.
The basic principle behind this dialog is that you should select the set of preferences you wish to modify from the Topic popup menu at the top. This changes the items in the rest of the dialog to show the preferences associated with that topic. When confronted with this, users would totally fail to realise that there were more preferences than those in the first topic. A group of "concerned citizens" (including myself) spent many hours complaining to the author (John Norstad) about this, and he eventually came up with version two of the dialog, shown below.
The grey box around the per topic controls gives the impression that those preferences are grouped and somehow distinct from OK and Cancel buttons and the Topic popup.
Later on John added arrows to the Topic popup, drawing even more attention to it as the most important control in the dialog.