Quick follow up to this - I noticed that pandoc was working fine in Rstudio 
for conversion of R markdown. If you mimic the command used by RStudio to 
generate the pdf on the command line, it works fine.

pandoc SCG.protocol.md --to latex --from 
markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures 
--output SCG.protocol.pdf --filter pandoc-citeproc --template 
/Library/Frameworks/R.framework/Versions/3.0/Resources/library/rmarkdown/rmd/latex/default.tex 
--highlight-style tango --latex-engine /usr/texbin/pdflatex --variable 
'geometry:margin=1in' --bibliography SCG.protocol.bib

Not sure if this provides any more insight to the original issue.

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