I think the issue may be caused by HTML markup errors that prevent validation of the page as XHTML 1.0-Transitional.
In particular, in menubar.php, the flagcounter does not appear to be inserted with all tags correct.
Currently, it has <li><a href="http://s06.flagcounter.com/more/9Bq"><img src="http://s06.flagcounter.com/count/9Bq/bg_FFFFFF/txt_000000/border_CCCCCC/columns_1/maxflags_12/viewers_0/labels_0/pageviews_0/flags_0/" alt="Flag Counter" border="0"></a><br>
and should likely have <li><a href="http://s06.flagcounter.com/more/9Bq"><img src="http://s06.flagcounter.com/count/9Bq/bg_FFFFFF/txt_000000/border_CCCCCC/columns_1/maxflags_12/viewers_0/labels_0/pageviews_0/flags_0/" alt="Flag Counter" border="0"/></a></li>
instead.
The other pages may have menu issues due to HTML formatting errors .. use the Valid HTML link at the bottom of eachpaget o urn the page through the validator and spot the errors.
Hope this helps...
Best regards,
Ken