Wow! Awesome feature. I always wondered why rocks that I pictured to be larger than the gems could stack to 50 deep, yet tiny gems took up a full 16th of most bags. :)
However, it appears that if you have any identically named, yet "old version" gems around, you can't make them stack with any amount of dropping and picking them up again. (So this may apply only to newly mined gems, not sure.)
Nerd, are you sure? as soon as I saw the news on Global, I just dragged some old diamonds (as in, sitting in my bag forever) over each other, and they stacked. On some other threads, it's suggested to reload - several times. Maybe it will just take some time to smooth out.
Stacking appears to be related to a street change type reload. Once I picked up my unstackable gems and left my house with them they would stack. It's now working for me. Hope this helps someone else.
For my existing gems, mine wouldn't stack until I left my region for another. Just exiting my house onto a street didn't allow me to stack them. For some reason you have to physically carry the bag with the gems in it with you and travel out-of-region then they will stack. Go figure.