I took a look at the site (the link to your themes.php page only works if you are logged in).
The problem is that you are aligning the images to the left or right. The is basically the same thing as floating them in the CSS. It has the side effect of not allowing them to push down other content like they should.
In other words, unlike adding a normal image, which will simply push everything below it down, if an image is aligned to the left or right, its height has less of an effect on the surrounding objects unless otherwise defined.
To put it even easier ?? Here are 2 good options:
1) Do not align the images to the left or the right
or
2) Add this to the bottom of the posts with images (be sure to use the code editor – not the visual editor – in WP):
<div style="clear:both;"><!-- --></div>
That forces the floats to clear, and pushes the content down the way it should be.
Also, you could add that code to your theme files, below sections of code where posts are listed (index.php, archives.php, etc..) but there would be a bit more involved.
Hope that helps.