Source map support has been expanded. Previously, it was just supported for going from minified, bundled code to the unminified, bundled code. If optimize: 'uglify2' is used, it will now go back to the separated, unbundled files.
Source map support is still considered experimental though, so you may find bugs. If you find one, file an r.js issue, ideally with a test case.
Full list of changes for 2.1.6: