Featured Image overriding Media Editor

Does the current media editor interact with the Featured Image/post-thumbnail function at all? Featured Image seems to ignore any edits I make, which seems weird.

In WP 3.2.1, I’ve been uploading an image, then using the built in Edit Image button to crop a new thumbnail. When doing so, I choose that it will apply to the Thumbnail size only (instead of All image sizes.) Hit save, and the thumbnail appears to be updated correctly, at least in the Media Gallery.

However, setting this as the Featured Image, or choosing it as the Featured Image later on, results in an automatically cropped thumbnail. The size is the correct size I have specified in functions.php, but it’s a new thumbnail image, not the one I made in the Media editor.

Is this doable? Will featured image only pay attention to my editing if I apply the crop to all image sizes (which won’t work in this case.) I used to be able to use my custom cropping with the scissors plugin, but that kills the TinyMCE interface now, so I’ve disabled it.

Thanks for any help people can provide.