Hi there!
I noticed that the Show Menu Bar Window shortcut is ctrl + shift + cmd + M but according to the settings it should be ctrl + option + cmd + M. You can see that in the screenshot below. I tested this with the op Show Hookmark Menu Bar Windows turned on and off.
The second problem is that the shortcut overlaps with that of Copy Markdown Link.
I checked for custom shortcuts I may have set in Settings > Keyboards but non where set.