I have just changed to Sierra - 10.12.4
Some apps (e.g. Aquamacs, Moneywell) in the Dock when you start them do not get a mark saying they are running but create a new icon that represents the running instance. This icon seems to have as its app one under /private/var/folders but with the correct app name not one in /Applications
Why is this happening and how can I get things back to how previous OSX versions worked.