For anyone searching for an answer to this problem, the thing you’re likely missing is that you haven’t selected a featured image for the product.
Take a look at the code of your non-working image in firebug. You’ll see a <figure> with an <a> inside. Inside the <a>, you’ll see two divs with a class of product-image. Notice in the code, the first div.product-image is empty. The second has an image in it — the image that you’re seeing!
So while you’re tempted to think “it’s showing my first image, but not the second”, what you’re seeing is actually your second image (first gallery image). The “first image” (the featured image which you haven’t set) is just not being output by WP because it doesn’t exist.
Go set a featured image and be happy.
