I'll try to summarize what I understood from your post so that I ensure that we are on the same page.
You are successfully changing the Windows8Palette's colors by using the approach we recommend in our documentation
-- by setting custom values for the color properties of the Palette object. What happens next is that at some point (for example on a new popup or window you want these colors to be different but if you just change them the way you did this will affect your whole application as the Palette is a global singleton). Unfortunately there's no easy way to accomplish color variation of the theme per control/window only. This was already discussed on another thread
stating so I really recommend that you look into it and the proposed solution.
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