Alrighty for the lightbox captions make sure you fill out the alt and title text of your featured image as you upload it. If you forgot to then you can click the image when editing your post and fill out the texts.
Next open up /wp-content/themes/[your_theme]/lib/shortcodes/15-portfolio.php and on lines 243 - 256 you should see this,
$out .= mysite_display_image( array(
'src' => $img[0],
'alt' => '',
'title' => '',
'height' => $height,
'width' => $width,
'class' => 'hover_fade_js',
'link_to' => $link_to,
'link_class' => 'portfolio_img_load',
'prettyphoto' => ( empty( $_post[$id][0] ) ? true : false ),
'group' => $img_group,
'preload' => true
) );
Change it like this,
$meta = get_post(get_post_thumbnail_id($id));
$out .= mysite_display_image( array(
'src' => $img[0],
'alt' => get_post_meta(get_post_thumbnail_id($id), '_wp_attachment_image_alt', true),
'title' => $meta->post_title,
'height' => $height,
'width' => $width,
'class' => 'hover_fade_js',
'link_to' => $link_to,
'link_class' => 'portfolio_img_load',
'prettyphoto' => ( empty( $_post[$id][0] ) ? true : false ),
'group' => $img_group,
'preload' => true
) );
And then do the same for lines 573 - 585.
I'll add this to our queue and we'll see if we can get it added in a future update.