Hi! I've also had this problem (with 0.4). It all worked fine on my local machine but when I migrated to a live site I encountered this problem. The second Featured Image would upload and appear in the correct edit screen box but would then just disappear when you clicked 'update'. Although I had a custom post type this was functionality was only used on the main 'post' type.
FYI I have the following other plugins:
I did manage to fix this but I'm not sure how. Here's two things I did:
1. Rename the plugins directory to something else and create a dummy plugins folder. Then visit the plugins admin page which had errors due to not finding the plugins. Delete the plugins directory and rename the old one back then visit the page again.
2. I tidied up my code in functions.php and rearranged the order a bit. I finally settled upon:
// Add support for extra Artists Portrait Image
$thumb = new MultiPostThumbnails(array(
'label' => 'Artist-Portrait',
'id' => 'artist-portrait'
add_image_size('artist-portrait-image', 337, 246, true);
// Add support for Post Thumbnails/Featured Image
add_theme_support( 'post-thumbnails', array( 'post','print_images','page' ) );
set_post_thumbnail_size( 250, 180, true ); // true = hard crop mode
add_image_size( 'menu-thumbnail', 64, 64, true ); //
add_image_size( 'featured-image', 247, 246, true ); //
add_image_size( 'artists-page', 267, 170, true ); //
add_image_size( 'random-print', 260, 157, true ); //
add_image_size( 'wide-page', 612, 246, true ); //?>
Before I did have a comma after 'id' => 'artist-portrait'
Anyway, great plugin. And it seems to be working for now. I hope you can work out the issue for 0.5