It's good that you've "seen the light" and are changing your practices. Your issues aren't really related to PHP. They're more HTML errors. Your navigation currently is coded like this:
HTML Code:
<ul
<li><a href="http://integralbuddha.net/index.htm" class="current" target="_top"
<li><a href="http://integralbuddha.net/topics.htm" target="_top"
<li><a href="http://integralbuddha.net/research.htm" target="_top"
<li><a href="http://integralbuddha.net/audiovideo.htm" target="_top" & Video</span></a></li>
<li><a href="http://integralbuddha.net/reading.htm" target="_top"
<li><a href="http://integralbuddha.net/links.htm" target="_top"
<li><a href="http://integralbuddha.net/creativeart.htm" target="_top" Art</span></a></li>
<li><a rel="nofollow" href="http://integralbuddha.net/forum.htm" target="_top"
</ul>
It should be like this:
Code:
<ul>
<li><a href="http://integralbuddha.net/index.htm" class="current" target="_top"</li>
<li><a href="http://integralbuddha.net/topics.htm" target="_top"</li>
<li><a href="http://integralbuddha.net/research.htm" target="_top"</li>
<li><a href="http://integralbuddha.net/audiovideo.htm" target="_top" & Video</span></a></li>
<li><a href="http://integralbuddha.net/reading.htm" target="_top"</li>
<li><a href="http://integralbuddha.net/links.htm" target="_top"</li>
<li><a href="http://integralbuddha.net/creativeart.htm" target="_top" Art</span></a></li>
<li><a rel="nofollow" href="http://integralbuddha.net/forum.htm" target="_top"</li>
</ul>
The highlighted parts are what you're missing. An invaluable tool is finding mistakes like this is to validate your markup.
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