Cloner Plugin Not Updating Attachment URLS

I'm using the Cloner plugin to clone a subsite of my Wordpress multisite network. I'm running into two issues related to media attachments.

1. Embedded photos etc are not having their URL updated and are pointing back to the original source site.

Here's an example post:
http://historyinpieces.com/video/photos/jfk-inspects-model-kennedy-center

The embedded images are being pulled from the original source site at http://historyinpieces.com/research/ rather than the new site at http://historyinpieces.com/video/.

In the site settings, the Upload Path has been correctly set for the new blog number.

2. Image and media attachments are being copied but are showing as 404 errors in the new site. This isn't noticeable in the example in #1 because the URLs are still pointing to the old site.

But here's an example with featured images (the URLS for the featured images field is getting updated): http://historyinpieces.com/video/photo-galleries

As you can see, all of the thumbnail links are broken. And if you try to access the thumbnail directly it leads to a 404:
http://historyinpieces.com/video/files/2014/10/JFK-Meets-with-the-Earl-Mountbatten-6-February-1963-021-150x150.jpg

I have confirmed that the file does in fact exist and is visible through FTP access and are in the correct blog number's files area (eg. /wp-content/blogs.dir/##/files.

I see no permissions red flags, although it's possible the permissions aren't being set properly.

When the cloning is underway the plugin reports no errors and lists all of the attachments as copying ok.

I'm using WP 4.1.1.