I have seen the same contacts issue with the Message+ app on my Windows 10 desktop and laptop. The app apparently uses some version of the Cloud contacts list and is not synchronized completely with the Cloud and associated phone being backed up. I had done some troubleshooting with this and found it is using/creating an SQL database but tech support couldn't identify where it was built from.  My desktop Message+ app has photos and names of the contacts that don't match completely with the Cloud contacts.