Custom posts per page does not work with pagination

Use a pre_get_posts action in your functions.php with conditional tags, and remove the call to query_posts:

function wpa62751_pre_get_posts( $query ) {
    if ( is_category( 'my-category' ) && is_main_query() )
        $query->set( 'posts_per_page', 4 );
}
add_action( 'pre_get_posts', 'wpa62751_pre_get_posts' );

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