Thought I'd share this in case others may be experiencing the same issue.
I'm currently developing a new e-commerce site based on Arras with the WP e-commerce plugin. The main issue I've had thus far was pagination with a custom permalink structure but managed to track this down to the theme's page.php file. Removing the
arras_above_content() from the top of the file resolved the problem.
The site in question is here: http://qtcards.com
Hope that helps,