The dark theme uses a custom CSS file. If you want to keep the full customization of the dark theme and still change the background color, you'll have to make a copy of that dark CSS file and change it to reflect the new colors, save it somewhere on your site (outside the plugins folder, otherwise the settings will be lost on upgrade), and enter that URL in the "Custom CSS" option. When you use a CSS file, it overrides the color picker options because it allows you to change EVERYTHING, even a number of colors for which there are no settings.
If you only want to change the background color, here's probably the easiest way to do so:
* Add a new profile, based on the "Default" profile. Call it anything - "blue-theme" or whatever.
* After creating the new profile you're taken to the profile edit page. Now change the viewer mode to Enhanced, and the additional options become visible.
* Change the Page Area Background Color setting to the color you want, and save the profile.
* In your shortcode, make sure you select the profile you just created, either by its name or its ID number.
If you want this to apply to all documents, you can just change the default profile as above without creating a new profile. Then you don't need to specify a profile in your shortcode at all to use it.
Let me know if you need more help. Thanks!