I haven't seen the specific behaviour you describe... but...
Are you sure the window is active when you try to click on the menu? It is not a silly question... and I know it seems obvious but you should make sure... If your cursor is blinking in the inspector, then you window won't be active until the value is entered... even though the changes will effect what was selected.and sometimes I have found that I may have to click on the window to make it active or other mouse actions will not respond.
Thanks Lyndsay. I looked to see if that was the cause but it wasn't. I have only seen this at this client's site where I am using thier hardware and FileMaker install. I did update the FileMaker Pro 12 to the latest update myself there so I don't think it is an issue with the install.