I am having a similar problem but I am NOT copy and pasting. I am using a blog editor (Qumana) and WordPress is changing the HTML when I upload. This is really frustrating. How do I get it to leave my HTML alone?
please let me know if there are other links I can post that will help this process out. For instance, here are the two files that contain the code (the same placed and code as in the blog that is working).
http://pricednostalgia.com/pnwordpressfiles/wp-content/themes/wpthemegen/header.php
and
http://pricednostalgia.com/pnwordpressfiles/wp-content/themes/wpthemegen/sidebar.php
