How an additional parser breaks my LaTeX code

LaTeXparsingInRhelpFiles.tex

% This is how it should look
\eqn{LaTeX code goes here}{%ASCII fallback text goes here
}

% This is what it looks like after a parser forcibly applies a hard line break
\eqn{LaTeX code goes here}{%ASCII fallback
text goes here
}

Note how lines 2 and 3 mean that nothing after the % sign should end up as TeX output. By contrast, when the TeX parser gets to line 7 it will try to render those words and typeset them in TeX.