Thanks for the good words – I’m happy you find the enhanced search capability useful.
Both the Featured Image and the Insert Media windows are part of the Media Manager Modal Window (MMMW). There is no standard way to extend the MMMW toolbar, and there are conflicts among plugins that add controls to it. One thing you can check is for other plugins that add features to the toolbar. Here are some earlier support topics on MMMW issues:
MLA and ACF image upload conflict
category selection when uploading media
Hide edit cat and tags in media manager
Problem with Simplefields
filter not showing in modal popup window for image
Plugins with known issues include Advanced Custom Fields, Media Categories, Simple Fields and Image Widget.
Another thing to consider is the width of your MMMW display. If you make the window too narrow, the search box moves down underneath the attachments thumbnails area and becomes invisible. Make sure you have a wide enough window to make room for all the controls.
Finally, you can disable the MLA enhancements and verify that the standard WordPress search box appears in the window. You can also disable the MLA enhanced search box but leave the other controls in place. That might narrow down the problem.
I am changing the way MLA interacts with the MMMW in my next release, and there’s a small chance my improvements will help resolve your issue. If you’d like to test the improvements I make, please send me a note with your e-mail address and I will give you a copy by return e-mail. You can use the Contact Us page at our web site:
Fair Trade Judaica/Contact Us
Thanks for your interest, your understanding and your patience.