Very strange indeed. Do you have e.g. anti virus software running at all on these systems?
It still does looks like some anomaly in Sierra. I really would like to find out more so if you could send me the outcome of plutil -p ~/Library/Preferences/com.apple.dock.plist again, but now after you have restarted the system (and with the second icon still in the dock after that reboot). That should tell us where the OS thinks PM is/was.