No one knows train problems in Bavaria more than me, but then again I’m on trains half of the day several times a week. The system is nearly always on time, however, things do happen and you should be prepared. I frequently check to make sure there is no maintenance scheduled for the trips that I make since that can make a dramatic difference in how your day progresses.
The reason I’m pointing this out now is that I was thinking about the hordes of tourists heading to Salzburg starting today because their Christmas market opens a week before everyone else’s markets. The problem is that there is maintenance scheduled along the tracks at the moment. The good part is it should be back to normal after the 26th. For more information directly from DB (the German train company) have a look here.