It seems I found a workaround for the above problem.
While I found no support from VStep,Steam, Avanquest (the company that provides technical support as printed on the DVD) and the seller on Amazon I just remembered the above comments that the latest update was mainly for the german version.
In Steam you can configure a few things for Ship Simulator Extremes, one amongst them is the game language.
So I switched to English and retried one of the uncompletable missions. The first mission objective was to moore to another ship, and the completion was acknowledged so I could move on. Don't have the time to play right now though.
So assuming the same applies for the other missions I can say that switching to English solves issues. :-)