Hi Dave
You have to press "Apply Globally" (or hit F6). Yes this may sound counterintuitive, as most applycations set preferences with modal windows, or always remember the last input you wrote. But, as you may have seen, in PixInsight "Global Perferences" is just like any other process. It has the same window, even with the drag and drop object. This means that you may create a icon with your favourite settings, and save them to a disk file, or even have several setting sets, for different types of project.
Was I'm trying to say, is that it is a bit odd, it does make sense in PI's GUI, once you are familiar with its methods.