I am seeing the message "The application RescueTime is not open anymore."
The OS X system message "The application RescueTime" is not open anymore" can be confusing because it doesn't mean what you might think!
It doesn't mean RescueTime isn't running, it means that an instance of RescueTime is open and running already, and you have tried to open a second instance of the application. If you see this message, make sure that RescueTime is running on your computer—look for the RescueTime icon in your OS X Menu Bar at the top of your screen.
If you do not see the RescueTime icon, you should download and install a new copy of the application, making sure to follow the steps for enabling accessibility permissions.