I’m having a similar problem with the right sidebar appearing below the article summaries except that it only happens on page 2 of the article listings. The home page is fine.
I am using a “single column-two columns-three columns” front page layout with 6 posts per page (version 3.0.3)
There seems to be a missing div tag that only disappears in second and subsequent pages but I cannot find where and how this happens. If I add a closing div tag to the second sidebar template that fixes the problem on the second page but it then appears on the home page.
Any suggestions/fixes would be appreciated.