I am using the german Wordpress 3.5.1–de_DE with Woocommerce 2.0.8 and the Woothemes Mystile Theme 1.2.8.
I have a big picture for a product (Jellyfish.jpg) and want to use a specific area of that big picture as a thumbnail, because Wordpress/Woocommerce automatically chooses a not useful part of the image. So I used the Wordpress crop tool in Edit Image under Media to generate a 150x150 thumbnail. This sucessfully generates a thumbnail (like Jellyfish-e1367238219134-150x150.jpg) but WP/Woocommerce uses another image (Jellyfish-150x150.jpg).
On my FTP I found the following files in /wordpress/wp-content/uploads/
012 KB 0666 29.04.2013 14:56 Jellyfish-150x112.jpg
015 KB 0666 29.04.2013 14:56 Jellyfish-150x150.jpg
026 KB 0666 29.04.2013 14:56 Jellyfish-300x225.jpg
082 KB 0666 29.04.2013 14:11 Jellyfish-787x300.jpg
009 KB 0666 29.04.2013 14:56 Jellyfish-90x67.jpg
017 KB 0666 29.04.2013 14:23 Jellyfish-e1367238219134-150x150.jpg
016 KB 0666 29.04.2013 14:58 Jellyfish-e1367240287874-150x150.jpg
758 KB 0666 29.04.2013 13:34 Jellyfish.jpg
I searched in the template and the plugin but it seems like they simple just use the_post_thumbnail and output the Jellyfish-150x150.jpg image (which is the useless autogenerated thumbnail).
Am I doing something wrong? What is the Jellyfish-e1367238219134-150x150.jpg image for? How can I choose which part of the image I want to show as a thumbnail?