convert-ly adding linefeeds / carriage return

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Good evening,

I have just upgraded to the latest Lilypond, version 2.19.16. I'm using Frescobaldi 2.18 on Windows 8.1.

Running convert-ly on any of my Lilypond scores, I find that carriage returns and/or linefeeds get added to each line.

This:

\version "2.18.2"

\include "_paper_setup.ily"

\include "_slash_notation.ily"

% Define header and footer

\header {

  title = \markup \bold \larger "My Song"

  composer = \markup \large "Music by John Doe"

  poet = \markup \large "Lyrics by Jane Done"

  }

}

Becomes this:

\version "2.19.16"

\include "_paper_setup.ily"

\include "_slash_notation.ily"

% Define header and footer

\header {

  title = \markup \bold \larger "My Song"

  composer = \markup \large "Music by John Doe"

  poet = \markup \large "Lyrics by Jane Done"

  }

}

I have never run into this problem before and couldn't find anything similar searching the list. Any ideas?