Sorry for resurrecting an old thread here, but I had a similar problem with Woocommerce that I think I have found a workaround for.
Product image sizes set in Woocommerce were being ignored, and product images were being displayed at grossly magnified sizes regardless of thumbnail settings.
However, after a bit of Googling I tried adding this code to ATO/CSS inserts and it seems to have done the trick:
Code:
.woocommerce ul.products li.product a img, .woocommerce div.product div.images img {
width: auto;
}
Might be of help to the OP or others with similar issues?