Your solution worked for me on version 24.5, but now that I'm in version 24.7, I've got the same problem. And this time, restoring the settings as you described does not solve my problem. Curiously, Stamp Visible works fine in the Beta version (25).
Responding to Jane-e, that only works if I select layers, then click and hold on merge visible, then press Alt before releasing the mouse button. If you press the Alt key at any time prior to that, the menu dropdown disappears!
It's a reasonable workaround for the time being, but it's awkward. I still prefer the old ctrl-shift-alt-e, which has worked for years.
I would also point out that ctrl-shift-alt-e works fine in the 2022 version.
I've seen a couple of other reports of this, so it's not just you. "Stamp Visible" is not actually a menu command. Before Adobe gave us the ability to add Alt/Option to the Merge Visible shortcut, we had to copy the layers, then hide half of them.
Cory is on this thread, so we know that it's on Adobe's radar.