From the ÖBB website:
Traffic restriction Salzburg Central Station – Freilassing – Munich Central Station
From 27th November 2015, Railjet trains will recommence service to Munich. To enable complete governmental monitoring of passengers, travelers from Budapest/Vienna coming into Salzburg must change to a Railjet train provided on the same platform to carry on to Munich. Border control will be carried out during the change. Railjet trains are travelling directly from Munich to Budapest via Vienna without a change. The ÖBB request that all passengers travel with applicable travel documents for the border crossing between Austria and Germany. Local traffic, which crosses the border between Salzburg and Freilassing is running according to a special timetable.