Ho risolto il problema usando
TMEdit v1.0 RC2 (ex HTMLArea)
http://www.xhtmlsuite.com/tmedite riconfigurando
popups/ImageManager/config.inc.php
$BASE_ROOT = "subdir/images/stories";
popus/Insertfile/config.inc.php
$MY_DOCUMENT_ROOT = $_SERVER['DOCUMENT_ROOT']."/subdir/images/stories";
$MY_BASE_URL = '/subdir/images/stories';