Issue with rewrite rules and subfolders [was Why? Help... see inside, please]

 /**
   * name: getDocumentObject  - used by parser
   * desc: returns a document object - $method: alias, id
   */
  function getDocumentObject($method,$identifier){
    global $changed;
    global $myObject;
    $tblsc = $this->getFullTableName("site_content");
    $tbldg = $this->getFullTableName("document_groups");
    // get document groups for current user
    if($docgrp = $this->getUserDocGroups()) $docgrp = implode(",",$docgrp);
    // get document
    $access = ($this->isFrontend() ? "sc.privateweb=0":"1='".$_SESSION['mgrRole']."' OR sc.privatemgr=0").
      (!$docgrp ? "":" OR dg.document_group IN ($docgrp)");
    $sql = "SELECT sc.*
      FROM $tblsc sc
      LEFT JOIN $tbldg dg ON dg.document = sc.id
      WHERE sc.".$method." = '".$identifier."'
      AND ($access) LIMIT 1;";
    $result = $this->db->query($sql);
    $rowCount = $this->recordCount($result);
    if($rowCount<1) {
      if ($this->config['unauthorized_page']) {
        // check if file is not public
        $secrs = $this->dbQuery("SELECT id FROM $tbldg WHERE document = '".$identifier."' LIMIT 1;");
        if($secrs) $seclimit = mysql_num_rows($secrs);
      }
      if ($seclimit>0)  {
        // match found but not publicly accessible, send the visitor to the unauthorized_page
        $this->sendUnauthorizedPage();
        exit; // stop here
      }
      else {
        // no match found, send the visitor to the error_page
        $this->invokeEvent('OnPageNotFound');
        $this->documentIdentifier = $this->config['error_page'];
        $this->documentMethod = "id";
        $this->documentObject = $this->getDocumentObject(
            $this->documentMethod,
            $this->documentIdentifier
            );
        $changed = 1;
        $myObject = $this->documentObject; 
      }
    }
    if ($changed) { return $myObject; }
    if($rowCount>1) {
      // too many matches found, send the visitor to the error page
      $this->messageQuit("More than one result returned when attempting to translate `alias` to `id` - there are multiple documents using the same alias");
    }
# this is now the document :) #
    $documentObject = $this->fetchRow($result);

    // load TVs and merge with document - Orig by Apodigm - Docvars
    $tbn = $this->dbConfig['dbase'].".".$this->dbConfig['table_prefix'];
    $sql = "SELECT tv.*, IF(tvc.value!='',tvc.value,tv.default_text) as value ";
    $sql.= "FROM ".$tbn."site_tmplvars tv ";
    $sql.= "INNER JOIN ".$tbn."site_tmplvar_templates tvtpl ON tvtpl.tmplvarid = tv.id ";
    $sql.= "LEFT JOIN ".$tbn."site_tmplvar_contentvalues tvc ON tvc.tmplvarid=tv.id AND tvc.contentid = '".$this->documentIdentifier."' ";
    $sql.= "WHERE tvtpl.templateid = '".$documentObject['template']."'";
    $rs = $this->dbQuery($sql);
    $rowCount = $this->recordCount($rs);
    if($rowCount>0) {
      for($i=0;$i<$rowCount;$i++) {
        $row = $this->fetchRow($rs);
        $tmplvars[$row['name']] = array($row['name'],$row['value'],$row['display'],$row['display_params'],$row['type']);
      }
      $documentObject = array_merge($documentObject,$tmplvars);
    }
    return $documentObject;
  }