First of all, I am no wiz when it comes to WP, but I managed to edit the classic theme a little so it's a little easier to grasp, and so I was helping a friend to customize her wp.
Her site: http://jadedrose.net/wp/
The error we encountered was this:
When not using the comments pop-up window, the comments field was pushed to the left of the page, and not showing up where the blog is.
The files I've edited is header.php, index.php and comments.php. If any coding from these three is needed to help me out, let me know and I'll post it.
We managed to solve this on our own, it seems that it was a <br> tag who caused the error.