As per the subject, when a heading line is included within a `#+BEGIN_EXPORT backend ... #+END_EXPORT' block, it breaks the parsing of the block, which is instead split into multiple `paragraph' elements.
See the attached example (test.org), and associate exports (test.tex) and (test.html). Tested with `emacs -Q -l minimal-org.el', with the org package installed from http://orgmode.org/elpa/, org-20161102.
* Test heading
#+BEGIN_EXPORT latex
Text which should appear in \LaTeX{} exports, but not HTML.
#+END_EXPORT
#+BEGIN_EXPORT html
* HTML only heading
Text which should appear in HTML exports, but not \LaTeX{}.
#+END_EXPORT
% Created 2016-11-03 Thu 11:34
% Intended LaTeX compiler: pdflatex
\documentclass[11pt]{article}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{graphicx}
\usepackage{grffile}
\usepackage{longtable}
\usepackage{wrapfig}
\usepackage{rotating}
\usepackage[normalem]{ulem}
\usepackage{amsmath}
\usepackage{textcomp}
\usepackage{amssymb}
\usepackage{capt-of}
\usepackage{hyperref}
\date{\today}
\title{}
\hypersetup{
pdfauthor={},
pdftitle={},
pdfkeywords={},
pdfsubject={},
pdfcreator={Emacs 25.1.1 (Org mode 9.0)},
pdflang={English}}
\begin{document}
\tableofcontents
\section{Test heading}
\label{sec:org0b53ca6}
Text which should appear in \LaTeX{} exports, but not HTML.
\#+BEGIN\(_{\text{EXPORT}}\) html
\section{HTML only heading}
\label{sec:org14261e8}
Text which should appear in HTML exports, but not \LaTeX{}.
\#+END\(_{\text{EXPORT}}\)
\end{document}
Table of Contents
1 Test heading
#+BEGINEXPORT html
2 HTML only heading
Text which should appear in HTML exports, but not \LaTeX{}. #+ENDEXPORT
Created: 2016-11-03 Thu 11:34
(setq user-emacs-directory "C:/Data/Documents/emacs.d/") (package-initialize) (require 'org)
