Finally I found a way, that seems to work so far. All the time since I use PM, I created a Photomechanic folder in the Apple Application folder where I put in the Extras, ReadMe.PDF and PhotoMechanic 5 App File. Now I, moved the PhotoMechanic App File out of this folder directly into the Application Folder.
I have no issues anymore with double Icon or inactive ghost icons. This does work on a iMac 5K OS 10.12.4 and on the new MacBookPro with PM build 18359.
Hope this does help you too, if you have the same issue.