Merge Stamp all visible layers

I'm trying to "Merge Stamp all visible layers" as Adobe calls, it by pressing Shift+Command+Option+E which normally works for me, but in this instance it's not. Is it because I'm using Smart Layers? I'd like to create a new rasterized layer that contains a merge of all of my previous/lower layers, without flattening all of the lower layers. I was able to do this by duplicating the Smart Layers, and then rasterizing that, but why won't Shift+Command+Option+E work, as it normally does?
Thanks in advance.

If I’m not mistaken having a SO selected should not make a difference – at least it does not for me.
The occasions where I’ve noticed the command does not work is when I have an invisible Layer selected, in which case command-alt-shift-N (new Layer), command-alt-shift-E usually suffices as a work-around.
Mind posting a screenshot with the Layers Panel visible?

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