instead of using custom sizes in your function.php (yah, i’m late sorry) why don’t you use (http://wordpress.org/plugins/simple-image-sizes/).
It create a subsection into your settings section, called “Media” and you can manually create different sizes with crop option.
Never forget to batch regenerate your images after this and it works!
The above link goes to an out-of-date address, so for anyone still looking for the solution, an explanation and links to the WooCommerce documentation is on our blog at http://www.cbdweb.net/woocommerce-and-image-sizes/
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