I just had the same problem with the comments page. In order to get the sidebar where it belonged, I had to make changes to both the post template and the stylesheet.
Here's how I solved it:
On the post template (single.php) added
<div class="ncol"> just under the initial <get header> call.
<div class="wcol"> that appears a few lines down.
<?php get_sidebar(); ?> just above the get_footer call at the very bottom of the code.
My real problem was that the comments text and preview boxes were too wide. On the stylesheet, I had to reduce the comment preview, comment form text area and comment form submit button. 450 is about the same width as the narrow column text line up, so I used that.
Even though your lines on the page don't appear to be overlapping, I think you may be encroaching into some border areas. I'm really new at this so I might be wrong...
I fully understand your frustration. It took me hours. I had things so jacked up I had to paste the original single.php code into WP and start over--twice.
Your situation may be entirely different, but maybe this will give you a starting place.
Hope this helps.