The issue is that thumbnails which are created by the plugins don’t have a _wp_attached_file entry in the _postmeta table, which manually created thumbnails do.
The solution to the problem in to do the following:
1: Open your media library in WordPress and delete all of the the grey, unattached images which do not appear to have a thumbnail. They should look just like the ones in the picture in this post.
2. You’ll have to edit the plugin for this one so fire up your FTP client and download whichever of the two plugins you are using.
Open the plugin in your favorite editor and locate the code below. In auto-featured-image.php it’s line 202, and it’s line 258 of auto-post-thumbnail.php
wp_update_attachment_metadata( $thumb_id, wp_generate_attachment_metadata( $thumb_id, $new_file ) ); return $thumb_id;
Replace it with the code with the following:
wp_update_attachment_metadata( $thumb_id, wp_generate_attachment_metadata( $thumb_id, $new_file ) ); update_attached_file( $thumb_id, $new_file ); return $thumb_id;
Upload the plugin to your site, find the settings page for your plugin and hit the “generate thumbnails” button. Now sit back and wait while the plugin regenerates all of the thumbnails again.
Thanks to misthero for originally finding the solution for the Auto Post Thumbnail plugin.