The default 1.9 product magnifier is not initialising properly on page load. But does initialise when a thumbnail i.e. .thumb-link is clicked.
I have done a diff on the difference between .product-image and it's descendants before and after manual initialisation of the magnifier by virtue of clicking on a thumbnail.
The difference is the addition of zoom-available to the product-image class as well as visible to the gallery-image class.
That class is added to the element depending upon the dimensions of product image. Check the dimensions of both images, one that can't magnify and one that can. You'll be able to see the difference easily.
I remember seeing this hardcoded in somewhere in a JS file, my first guess would be app.js as that does most of the heavy job in that Magento version. You can update that per your requirements.
Just remember to make it big enough so that you don't actually end up serving zoom for very small files. After all that's why it was applied in first place.
