Arkadaşlar çözümü deneye deneye buldum. Belki aynı sorunu yaşayan olur diye paylaşıyorum.
<ul class="nav navbar-nav">
<?php
$menusor=mysql_query("SELECT * FROM menuler where menu_bolum='AnaMenu' ORDER BY `menuler`.`menu_adi` ASC");
while ($menucek =mysql_fetch_array($menusor)) {
$altmenusor=mysql_query("SELECT * FROM menuler WHERE menu_bolum='AltMenu' and menu_katid='".$menucek['menu_id']."' ");
?>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false"><?php echo $menucek['menu_adi']; ?>
<?php if(mysql_num_rows($altmenusor)!=0){?>
<span class="caret"></span>
<?php } ?>
</a>
<?php if(mysql_num_rows($altmenusor)!=0){?>
<ul class="dropdown-menu">
<?php
while ($altmenucek=mysql_fetch_array($altmenusor)) { ?>
<li><a href="#"><?=$altmenucek['menu_adi']?></a></li>
<?php
}
?>
</ul>
<?php } ?>
</li>
<?php } ?>
</ul>