There are different types of markers. There are the ones that you place in the timeline, and those that are placed in a specific clip or graphics. As far as can tell, you can't actually select a clip marker, so there is no way for the application to know it's the target of the keyboard shortcut.
Timeline markers, on the other hand, can be selected; when they are selected, and only then, will command-option-M trigger the Edit Marker window.
I believe that this is just as the app is designed, and it has always been like that, but if I am wrong I expect that I will soon be put right.
In any case, if you feel this is wrong, you can let Apple know by using feedback:
Motion->Provide Motion Feedback