Remove the filter from the the_content and run it after the shortcode are processed.
Try:
remove_filter( 'the_content', 'wpautop' );
add_filter( 'the_content', 'wpautop' , 12);
Usually shortcodes are processed after wpautop is applied to the content. See http://core.trac.wordpress.org/browser/tags/3.1/wp-includes/shortcodes.php#L296
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