Thanks for using the plugin and for your kind words. If there are other features you'd like to see, let me know.
Now, on to the problem. Your message is the first report I've had about problems with the where-used reporting.
The "Bad Parent" notation means that the item is attached (i.e., the post_parent database field is not zero), but either the parent ID is for a post or page which has been deleted or the parent ID exists but the attachment is not used as the Featured Image and is not inserted in the body of the post/page. There are some problems with this field; for example, if you change the "Featured Image" for a post the post_parent doesn't always get updated. It's quite possible that there's some way to use an item that I am not yet searching for.
The "Orphan" notation means that my search did not find any post or page which uses the item as a Featured Image or has the item inserted in the body of the post/page.
I'll need more information to reproduce the problem and fix it. Can you tell me what's in the "Featured in" and "Inserted in" columns of the MLA listing for the problem items? What's in the ID/Parent column?
For one of the problem items, how is it used in the post/page that should be its parent?
The best way to help me look into this would be to send me some screen shots of the problem(s), e.g., the MLA listing page and the HTML view of the post/page content where the item is used. If you're willing to do that or you have other information you don't want to post here, go to the Our Story/Contact Us (http://fairtradejudaica.org/our-story/contact-us/) page at fairtradejudaica.org and give me your e-mail address. I'll send you my e-mail address and we can exchange more information.
Thanks again for using the Media Library Assistant and for your pateince while I work on this issue.