I just finished making an Action with 100s of actions when I realized it's not registering the duplication of folders. I ran some tests, and when I RIGHT click on the layers and select Duplicate Layers from the pop up, it DOES register in the actions.
However, when I use Ctrl + J to do the same thing with the shortcut, it does NOT register in the Actions.
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Addendum: Not sure if related but, a few months ago, suddenly all my Actions disappeared which was quite devastating. I thought it was an update, but I checked and apparently I do have automatic updates turned off, so I'm not sure what happened.