Ok your having two issues here.
One your getting duplicates, your saying this a software issue. We are trying to work out if just corrupted signals, if so its not a software issue but there may be a way to hande it.
Secondly the routes issue. Can you check the aircraft which have the wrong route, whether they landed at EHAM or another airport close to you and then change there Flight ID. As I think I am right in saying RB only checks the route when a new aircraft comes into coverage.