The theme uses WordPress’ built-in sanitation function to strip potentially harmful HTML data. Each field in the settings uses the wp_kses_data() function to sanitize user inputed content. (WordPress Codex has a good explanation concerning sanitation usage)
This is required for the theme to achieve approval by the WordPress theme reviewing team.
For a list of (default) accepted HTML tags and attributes, see the header of WordPress’ kses.php file.
This default behaviour can be overridden using plugins, theme or WordPress modding.
As far as modding the theme is concerned, you can edit the theme/admin/sanitize.php file and inside the [..]_options_validate() function you can remove the wp_kses_data() processing on every field you wish to remove the sanitation from (the field names are pretty much self explanatory).
Keep in mind these changes can affect your WordPress security.
Note: The presentation page columns and the 2 text areas below support shortcodes. The two titles above and below the slider do not.
Note 2: These instructions do not directly apply to Nirvana, which uses a differently structured sanitization code.