EDIT: Basically, I'm developing a little data processing gui that uses saved models to evaluate data and then plot the results. I have default models I want loaded at startup and to do this I'm using an initialization function in the opening function of the gui. (I created the gui using GUIDE) I also need to be able to change the defaults, and to do that, I created a Settings->Change Default Settings top menu that launches a Change Default Settings side gui. Using this side gui, I appear to be able to make the changes I need to make, however, they aren't saved. When I get back to the main gui, I can clearly see that the default settings are still loaded. If I go back to try and change the settings again, the defaults are listed as the loaded settings. I'm not sure what is really happening, but it appears as if my initialization function is being ran after I change the settings, thus undoing the changes I make. I don't know of any other way to load defaults without them always being reloaded.
I don't know if it helps, but I'm passing the main gui's handles structure to my initialization function to set the defaults.