Looks like you are having multiple copies of Priority Matrix on your Mac. Could you please click “Yes, quit another copy” and then delete another application from your Mac to make sure that only the latest version of Priority Matrix is available?
To find all the copies on your Mac, go to the search box and type in Priority Matrix – it will show you all the items with their location –
Remove the ones that are not in the Application folder and hopefully you should be good to go! However, there is one more thing you might want to look at. It is possible that you’re telling Priority Matrix to launch on start in two different ways. The first one is via the dock. Right click on the PM icon on your Applications folder or your system dock, and under “Options”, see if entry “Open at Login” is enabled. If so, feel free to disable that one.
Similarly, if you open Priority Matrix and go to the main menu, is entry “Launch on Start” enabled? It’s a good idea to keep only one of these options on, to prevent the system from thinking that it has to open PM twice.
P.S. Whenever you download another version in the future, could you please click on “Move to Applications folder” when prompted? This way it will be automatically replaced and you will not get the message above.