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It's like creating of project. If you want to create many animations, you have to have some possibility to store all keyframes, image frames, backgrounds in separate folders for each project. That's why you have to save parameters of animation in settings file. This settings file is your base project file. If you are loading keyframe, the program takes only from this parameters which can be animated (all floating point type parameters). On page: http://sites.google.com/site/mandelbulber/getting-started#TOC-Initial-setup , there is a list of all animated and non-animated parameters. I decided to make this in that way because of many reasons. For example, imagine what happen if you want to change, for instance, image resolution or background texture. If all parameters will be saved/loaded from keyframes, you have to change the same settings in each key-frame separately. Next thing is that the program wouldn't know what to do with parameters which can't be animated.
You wrote that "Is there a reason you can't save a full set of settings with each keyframe?". All parameters are saved in keyframe files. You can load it as a settings file.