Ok -- so I seem to have found the source of the issue. In a Collection, Virtual Copies are not stacked automatically. However, in Library grid view, they are. Vitual Copies made in a Collection will be stacked in the Library folders.
I really wish there was an option for automatic stacking in a collection besides "Auto-Stack by Capture Time." Since I use collections as edits of my library folders and organize these selections using collections and collection sets, I do most of my development out of there. I seems strange that this automatic virtual stacking functionality only works in the Library...
Julieanne Kost @jkost, my Lightroom goddess, hear my prayers
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You've stumbled over LR's "unusual" stacking design. Stacking is specific to the folder or collection in which you made the stack. So if you make a stack in a folder, you can't view the stacking in the collection, and if you make a stack while in a collection, you can't view it in the folder. It is doubly weird that creating a virtual copy always creates the stack in the folder even when you're in a collection.
Many people have complained about this design; please add your me-too vote and details of your issue to this topic in the official Adobe feedback forum, where Adobe wants all product feedback: Lightroom: Stacking in folders and collections should be global | Photoshop Family Customer Community
Ok -- however, when creating a virtual copy in the collection you are working in, the copy with not automatically stack with the original in that collection. This was not stated specifically in your post above and I wanted to clarify.
Yes, it does seem inconsistent that virtual copies made while in a collection get stacked in the folder. I suggest you call that out if you post in the feature-request topic, where Adobe developers will see it (they don't actively participate in this forum).