Code removal causing issue – js_functions problem?

Hi all. We wish to remove popular posts from homepage. Each way we have tried this has caused there to be BIG gaps in our recent posts on homepage. Here is standard HP.

You will note the popular posts right at the top. Each time we remove the following code it creates bigs, we have looked in the js_functions and not found anything in particular disturbing, any suggestions would be most appreciated.

<div class="contentbox">
						<div class="boxheading"><span>popular</span><div class="clear"></div><div class="left"></div></div>
						<div class="blockborder" id="pop_border">
							<?php popularPosts(); ?>
							<div class="clear"></div>
						</div>
					</div>