Using a JSONFormatter (pretty) and JSON Writer in series, the output file contains literally the characters \\r\\n with no actual line returns. Snippet of the output:
"_formatted":"{\\r\\n \\"request\\" : [\\r\\n {\\r\\n \\"addDate\\" : \\"/Date(1449794160000-0600)/\\",......
Connecting an Inspector to the to the formatter works as expected.
I should mention that I am using the 2016.1 Beta version (for the Elasticsearch goodness it contains.)