This is still happening if any modifications are made to the commands menu. It happens only within files that are open at the time. If a new file is opened the tools are again responsive. The closing and reopening of the other files will remedy the problem without having to restart the program.
Tool palettes should update their contents when you change the command set. This does happen for all floating tool palettes but was not happening for the tool palette in the left sidebar. This will be fixed in the next WIP release. I cannot tell if this will fix the problem you are having with specific tool buttons.
Are you in multiple instances of Mac Rhino at one time? If so see the following…