Eu tive que atualizar manualmente para o pandoc 1.6, que corrige esse bug:
# Install and update cabal (Haskell's package manager)
sudo apt-get install cabal
cabal update
cabal install cabal-install
# Put cabal's executables to path
echo "PATH=${PATH}:${HOME}/.cabal/bin" >> ${HOME}/.bashrc
source ${HOME}/.bashrc
# Reset bash's path cache
hash -r
cabal install -fhighlighting pandoc