what you are describing here (cropped big size image in Edit Media screen) is a perfectly normal behavior when you use Apply changes to: All image sizes while cropping image and I believe the same thing could happen during upload when $crop param is set to true for all registered image sizes (similar to how add_image_size function works) As suggested above – deactivate image-related plugins and see what happens.
Anyway – the strangest thing is that there’s no Restore Original Image button in your screenshot. This button is exactly what you need to work with the original size in editor.
See the update below…
I can replicate this only AFTER I crop the image but BEFORE i save it. The Restore Original Image button appears there as soon as I come back to edit it again after saving it.
See my screenshot:
This is apparently not a final answer, but it doesn’t really fit the comment format so it ended up here…
UPDATE:
From looking at the source of image-edit.php it seems that a crucial role in decision whether to display the ‘Restore..’ link is a value of _wp_attachment_backup_sizes post meta field of a given attachment.
I would suggest checking that value for the problematic attachments. You can use something like this:
<pre>
<?php print_r( get_post_meta( $your_attachment_id_here, '_wp_attachment_backup_sizes', true ) ); ?>
</pre>
(or use the WordPress Console plugin)
Maybe you will find something odd there. Try also comparing these values between the broken and correctly displayed attachments… Again I know I’m not giving you the answer you’d like to hear but I believe this could be the right direction to investigate.
Cheers