An update to the Natural Earth dataset was released last week, and the MapBox geodata library has been updated to include it with TileMill-optimized versions of the new files.
The most noticeable change is that South Sudan had been given official independent status. There are numerous other improvements and corrections - see the Natural Earth blog for a fully-detailed changelog.
The 1.4.0 release has not replaced 1.3.0 in the MapBox library, but sits alongside it. The new files are available in new and existing installations of TileMill (version 0.4.0 or later), which is available for free download at TileMill.com.
For more information and questions about using the MapBox geodata library, visit support.mapbox.com.