The problem with using this plug-in is that the WordPress WYSIWYG Editor (TinyMCE), will remove any tags and attributes that it believes to be invalid according to it’s configuration. As two of the attributes used by this plug-in are custom attributes (escaped/line) they are removed, causing some unexpected output.

One solution to this problem is to add the custom attributes to the list of valid elements by using the ‘tiny_mce_before_init‘ filter and appending them to the ‘extended_valid_elements’ string.

The function below can be added to the functions.php file within your theme directory:

function tinymce_wp_syntax($init) {
	$values = 'pre[lang|escaped=true|line]';
	if (empty($init['extended_valid_elements'])) {
		$init['extended_valid_elements'] = $values;
	} else {
		$init['extended_valid_elements'] .= ','.$values;
	}
	return $init;
}
add_filter('tiny_mce_before_init', 'tinymce_wp_syntax');

Adding this to my blog enables me to continue using the visual editor instead of disabling it and at the same time will allow the other HTML filters to continue as normal .

Note: You may have to force refresh (ctrl + f5) the post / page editing page for the changes to take effect.

EDIT: This solution does not fully solve the problem in WordPress MU installations, as you need to adjust the allowed post tags used by the content filter.

if (!CUSTOM_TAGS) {
	$allowedposttags['pre'] =  array(
		'lang' => array(),
		'escaped' => array('true' => array()),
		'line' => array()
	);
}