How to display multiple $meta_boxes into separate tables

The Problem is in your ri_display_metaboxes() function more specifically this line:

foreach ($meta_boxes as $meta_box) {

Which tells WordPress to render both/all metaboxes on every single metabox display callback.

to get over it you can use the $callback_args parameter of add_meta_box function

so try this:

function ri_add_custom_box() {
    global $prefix, $meta_box, $meta_boxes;


    $prefix = '_ri_custom_meta_'; // a custom prefix to help us avoid pulling data from the wrong meta box
    $meta_boxes = array();

    $meta_boxes[] = array(  
    'id' => 'ri_meta_box_panel1', // the id of our meta box
    'title' => 'Test1', // the title of the meta box
    'page' => 'ri_my_page', // display this meta box on post editing screens
    'context' => 'side',
    'priority' => 'high', // keep it near the top
        'fields' => array( // all of the options inside of our meta box
            array(
                'name' => 'Test1:',
                'desc' => 'Test1',
                'id' => $prefix . 'Test1',
                'type' => 'text',
                'std' => ''
            ),
        )
    );

    $meta_boxes[] = array(  
    'id' => 'ri_meta_box_panel2', // the id of our meta box
    'title' => 'Test2', // the title of the meta box
    'page' => 'ri_my_page', // display this meta box on post editing screens
    'context' => 'side',
    'priority' => 'high', // keep it near the top
        'fields' => array( // all of the options inside of our meta box
            array(
                'name' => 'Test2:',
                'desc' => 'Test2',
                'id' => $prefix . 'Test2',
                'type' => 'text',
                'std' => ''
            ),
        )
    );

    foreach ($meta_boxes as $meta_box) {
        new Ri($meta_box);
        add_meta_box($meta_box['id'], $meta_box['title'], array(&$this, 'ri_display_metaboxes'), $meta_box['page'], $meta_box['context'], $meta_box['priority'],array('fields' => $meta_box['fields']));
    }
}


function ri_display_metaboxes($post,$meta_b) {
    global $meta_boxes, $post;

    echo '<input type="hidden" name="ri_meta_box_nonce" value="', wp_create_nonce(basename(__FILE__)), '" />';
    echo '<table class="form-table">';

        foreach ((array)$meta_b['arg']['fields'] as $field) {
            $meta = get_post_meta($post->ID, $field['id'], true);
            echo '<tr>', // create a table row for each option
                '<th style="width:20%"><label for="', $field['id'], '">', $field['name'], '</label></th>',
                '<td>';
            switch ($field['type']) {
                case 'text': // the HTML to display for type=text options
                    echo '<input type="text" name="', $field['id'], '" id="', $field['id'], '" value="', $meta ? $meta : $field['std'], '" size="30" style="width:97%" />', '', $field['desc'];
                    break;     
                case 'textarea': // the HTML to display for type=textarea options
                    echo '<textarea name="', $field['id'], '" id="', $field['id'], '" cols="60" rows="8" style="width:97%">', $meta ? $meta : $field['std'], '</textarea>', '', $field['desc'];
                    break;
                case 'select': // the HTML to display for type=select options
                    echo '<select name="', $field['id'], '" id="', $field['id'], '">';
                    foreach ($field['options'] as $option) {
                        echo '<option', $meta == $option ? ' selected="selected"' : '', '>', $option, '</option>';
                    }
                    echo '</select>';
                    break;
                case 'radio': // the HTML to display for type=radio options
                    foreach ($field['options'] as $option) {
                        echo '<input type="radio" name="', $field['id'], '" value="', $option['value'], '"', $meta == $option['value'] ? ' checked="checked"' : '', ' />', $option['name'];
                    }
                    break;
                case 'checkbox': // the HTML to display for type=checkbox options
                    echo '<input type="checkbox" name="', $field['id'], '" id="', $field['id'], '"', $meta ? ' checked="checked"' : '', ' />';
                    break;
            }
            echo     '<td>',
                '</tr>';
        }
    echo '</table>';
}