I only started with WordPress and the E-commerce plugin today, so I hope I’m posting this in the right place so that others can use it to fix their similar issue.
My problem was that the right sidebar moved to below the content, after a lot of searching I found that it had to do with the breadcrumbs because the problem disappeared when I turned that off.
After a while I tried to compare the source code of the page with breadcrumbs on and with them off, the line that was different ended with a closing div </div>. Conclusion: a div was being closed that wasn’t supposed to get closed since there was no extra opening div when the crumbs were turned on.
Finally I ended up in breadcrumbs.class.php around line 114 and commented out a closing div there: