In version 2.2.5 I cleared up the default settings in SlideMagic. The way things used to work were aimed at a professional presentation designer: the presentation settings including logo and colour were saved as default as soon as you save the presentation. I have changed that: defaults get saved in the background as soon as you make active changes to the settings yourself, loading and saving a presentation with different settings than yours does not impact your defaults.
I made a big effort to avoid the whole book keeping of colour templates and profiles. I think SlideMagic does the right thing in the background now, and given the few settings options there are, it is easy to adjust something if needed.
You can download the latest version here.