Hello,
convert.ly is not working as you described. Here are some code excerpts.
Let me know if there is anything else I can send that would be helpful.
From a file previously created with Frescobaldi 2.20 & Lilypond 2.18:
\version "2.18.0"
\include "
english.ly"
\include "Three White Gulls (Melody).ly"
\include "Three White Gulls (Verses).ly"
\include "Three White Gulls (Chords).ly"
\paper {
#(set-paper-size "letter")
system-system-spacing #'basic-distance = #15
markup-system-spacing #'basic-distance = #24