custom image size with New Media Manager in wordpress 3.5

You will need to paste your code in order for us to review where the issue is, however, I can demonstrate how I accomplish this in WordPress v3.5

Please observe the comments in my_insert_custom_image_sizes:

function my_insert_custom_image_sizes( $sizes ) {
    // get the custom image sizes
    global $_wp_additional_image_sizes;
    // if there are none, just return the built-in sizes
    if ( empty( $_wp_additional_image_sizes ) )
        return $sizes;

    // add all the custom sizes to the built-in sizes
    foreach ( $_wp_additional_image_sizes as $id => $data ) {
        // take the size ID (e.g., 'my-name'), replace hyphens with spaces,
        // and capitalise the first letter of each word
        if ( !isset($sizes[$id]) )
            $sizes[$id] = ucfirst( str_replace( '-', ' ', $id ) );
    }

    return $sizes;
}


function custom_image_setup () {
    add_theme_support( 'post-thumbnails' );
    add_image_size( 'custom-image-size-1', 160, 9999 ); //  small columned
    add_image_size( 'custom-image-size-2', 300, 9999 ); //  medium
    add_image_size( 'custom-image-size-3', 578, 190, true ); //  cropped
    add_filter( 'image_size_names_choose', 'my_insert_custom_image_sizes' );
}

add_action( 'after_setup_theme', 'custom_image_setup' );

Note that I am adding the my_insert_custom_image_sizes filter in the after_setup_theme which is a good practice.