Could this be a div problem surrounding the adsense code? I have seen many times when a </div> has been left out for instance, the div contents still show OK in firefox but not in IE.

You should use an HTML validation program to check your pages. I think you'll find the error(s) when you do it.

The closing div tag is there and the page validates XHTML 1.0 Transitional and CSS2.1 using the W3C validators.

Is it ok to post a link here to the my site without violating TOS?

Well I've narrowed the problem down to the theme. I turned all the plugins off and had the same problem. Turned them back on. Made the same changes in the default theme and it loads the adsense unit properly. So by process of elimination, that makes the theme the problem. I also know it's not any of the other mods I've made because it doesn't work properly in the original theme files either.

Here's my stylesheet: [thegadgitech.com...]

Here's is my wordpress loop (with some unrelated content hidden):
sorry, the tabs were stripped

<?php if (have_posts()) : while (have_posts()) : the_post(); ?>

<div class="entry<?php if(is_home() && $post==$posts[0] && !is_paged()) echo '_firstpost';?>">
<div class="latest<?php if(is_home() && $post==$posts[0] && !is_paged()) echo '_firstpost';?>">

<h2 id="post-<?php the_ID(); ?>"><a href="<?php the_permalink() ?>" rel="bookmark"><?php the_title(); ?></a></h2>

<div class="meta<?php if(is_home() && $post==$posts[0] && !is_paged()) echo ' firstpost';?>">
<?php _e("Posted on "); ?> <?php the_time('F jS, Y') ?> in <?php the_category(',') ?> by <?php the_author() ?> <?php edit_post_link('Edit', ' ¦ ', ''); ?>
</div>

<div class="main">
<?php if(is_home() && $post==$posts[0]) { ?>
<div id="topPostAdsense">
<!--GoogleAdsForContent TextAdUnits Begin-->
<script type="text/javascript"><!--
Google code here (hidden)//-->
</script>
<script type="text/javascript" src="http://pagead2.googlesyndication.com/pagead/show_ads.js"></script>
<!--GoogleAdsForContent TextAds End-->
</div>
<?php } ?>

<?php the_content(''); ?>

<?php wp_link_pages(); ?>

<ul class="readmore">
<li>readmore section/post footer (hidden)</li>
</ul>

</div>

<!--
<?php trackback_rdf(); ?>
-->
</div>
</div>

<?php comments_template(); ?>

<?php endwhile; else: ?>

<div class="warning">
<p><?php _e('Sorry, no posts matched your criteria, please try and search again.'); ?>
<?php include (TEMPLATEPATH . '/searchform.php'); ?></p>
</div>

<?php endif; ?>

I looked at your source code, and you have two divs with the same id="topPostAdsense", which will cause validation to fail. Something is causing a doubling of the topPostAdsense div in your code.

IE 6 has box model problems, and I'm guessing that your problem may also be related to this.

sorry, you got to it while I was testing. I copied the code and put it at the bottom of the page, just outside the loop. And it displays properly there. If you scroll down to the bottom, you'd see the ad below all the posts at the bottom of the page. But I've since removed that code, it was just to test and narrow down the problem, which seems to be something the theme is doing in the loop, but not outside the loop.

Got it down to a float problem. If I remove the float: right; statement, the ad is visible in IE6. But I really need the ability to float it to the right so the text content flows around it. Could adding a position: relative; statement to the parent div have any affect on floating elements? I will test that idea later.

Otherwise, I think I may go back to putting the adsense directly in the post - it floats fine there (or at least it used to on another theme). It's a little more work to keep up with, but then I can put the ad anywhere, not just the top-left or -right corner.