From a look at /wp-includes/default-filters.php:
Maybe one of the following filters is causing the problem. I’d try to remove_filter()
them and see what happens:
add_filter( 'the_content', 'wptexturize' );
add_filter( 'the_content', 'convert_smilies' );
add_filter( 'the_content', 'convert_chars' );
add_filter( 'the_content', 'wpautop' );
add_filter( 'the_content', 'shortcode_unautop' );
add_filter( 'the_content', 'prepend_attachment' );
If this doesn’t help, we’ll need another workaround.