Are all of the links for that part of the dynamic menu external? If so you can just remove the root url reference in the menu.php page. In this file you can find the dynamic links and just remove the root url reference.
Look for this:
php:
<?php do { ?>
<li><a href="<?php echo($assumedRoot); ?><?php echo $row_menuwriter_links["url"]; ?>"><?php echo $row_menuwriter_links["url"]; ?></a></li>
<?php } while ($row_menuwriter_links = mysql_fetch_assoc($menuwriter_links)); ?>
Change it to be like this:
php:
<?php do { ?>
<li><a href="<?php echo $row_menuwriter_links["url"]; ?>"><?php echo $row_menuwriter_links["url"]; ?></a></li>
<?php } while ($row_menuwriter_links = mysql_fetch_assoc($menuwriter_links)); ?>
