I don't believe settings work right in 2.44 anyway. Just load a saved sim and you can take the settings from that.
Settings work fine but not everything is saved into settings files (or sim files for that matter). I have followed a philosophy that makes a distinction between those settings which are specific to a particular simulation and those settings which are not. The former includes physics, costs, sim-options like field size, toroidal, no ties, fixed radii, species lists and so on. The latter includes things like window positions and sizes, which graphs are open, whether the display is on or off and viewing options such as shot impact dots, resource gauges and movement vectors. The state associated with these latter things IMHO should not be placed into either sim or settings files since they are really solely for the viewing pleasure of the human. They have no impact on the sim itself and they should in fact should persist across multiple sim invocations. You would not want all your graphs to close or your window positions and sizes to change every time you load a sim. Instead these things should be persisted in a sim-independent manner into their own INI file or the registry so that they persist across program invocations. Unfortunately, today they are not persisted at all. Doing this is on my list of work items but it is not high priority. I think that most people would agree that it is not an undue hardship to re-open a graph, resize a window or turn-off a viewing option once each time they start the simulator. I'll get to it someday, but not near term.