well the plugin is not designed to upload custom themes yet. The css files in the views/ directory are special templates wich are used to generate custom themes - changing these files will cause an unexcepted behaviour.
the currently best option is the following:
1. Instead of using the naming-scheme **_your_theme_name**EnlighterJS for the CSS classes, just use **EnlighterJS** - this will overwrite all theme settings
2. Add your Enlighter-Theme manually to your WordPress Theme as well as the EnlighterJS base styles
3. Go to the Enlighter Settings Page -> CDN
4. Deactivate the CSS Loading Checkbox
i will try to add an option to the next release which allows the use of custom themes (maybe an additional direcetory) and take a look onto the theme-customizer to check the background-color-issue.
thank's for your contribution & best reagards,