The two different crystals appear only in a few early episodes together. The non-standard one (the forward crystal in your image above) has a very different shape and size than the standard crystal, so it's easy to tell that it is only the standard one that appears from a certain point in the show onwards. I'm not sure what the backstory is regarding why, but having studied the geometry very closely, I can say with some confidence that the first one (which has a vertically symmetrical shape) just disappears early on and I don't think we see it again thereafter.
This is from "Where Silence Has Lease" 43:00
Standard crystal at right
This is from "The Schizoid Man" 31:14
Standard crystal in rear
"Unnatural selection" 00:45
Standard crystal forward (though it's a little hard to tell in this one because it's at such a distance and the Season-1 film grain is so bad.)