CC 2018 won't flatten all layers when the marquee tool is selected.

You're saying you created a custom kbsc for Flatten Image in the Layers menu/panel menu? I'm unable to replicate this at all. Creating a custom kbsc for the command, I've tried with the Marquee, the Ellipse, the Move, with layers selected and none targeted. I've also tried with a selection active, and that has no effect, either.

I think we need more information about what OS you're running. I'm on a Mac and this could be platform/OS specific. You may have some corruption in your Preferences, but you might prefer to wait and see what an Adobe person says about this before you purge your Prefs and start with a clean slate.

I can't reproduce here on Mac, using a custom shortcut (Opt + Shift + Cmd + F) for Flatten. Any other details on your system, the shortcut you're using?

Thanks all. I am on OS 10.2.6 and latest CC 2018 update. I am using a custom keyboard shortcut (shift + cmd + f). I was copying merged, creating a new doc, pasting as a new layer, and then wanting to flatten that via shortcut. Oddly I can't recreate it again myself today, but I haven't restarted or run any updates.