Hello Ihrsfo
Thanks very much for your input, very helpful perspective and apologies for posting in the wrong section, i am not on here all that frequently.
It does sound like Munich could be a lot slower to get through, which adds to the time difference. Interesting on the cross border fees, that is what i would expect given the proximity but I have heard stories of some fairly high charges, and I don't much like the thought of arguing with an agent who basically has you over a barrel!
The heavy traffic is also a concern for us but perhaps it would also be relatively heavy on the minor roads from Salzburg to Mittersill, i suppose you cannot answer that. Seems that maybe the extra saving on transfer might also be in getting the car too, which I hadn't really considered. We have been to Salzburg before and it is a small airport but this can often be a good thing as it means you can often get through much quicker.
Anyway, thanks for your help.