It happened to me, don't know if to others. But when I put thumbnails in the excerpt, it shrinks the space between the post boxes (I noticed it, because my post boxes are colored, so there was no white space between them). I used this code as example:
Code:
<div class='post-bodycopy'>
<img src="..." class='wp-post-image' />
<p>bla bla bla</p>
</div>
So I added a <br /> at the end of the </div> and it worked. It's a glitch? or it was just my installation