Yes, when it comes to saving, the distinction between a route and a session that is based on that route can be a source of much confusion - second only to route layers and session layers. The arrival of the Universal Driver Surveyor interface where you can exit Driver straight into Surveyor, edit, save, and then jump back into Driver where you left off has muddied the waters even further. Don't get me wrong, the UDS is a great feature and one that I am now frequently using, but it does have a trap that I have sometimes fallen into.
You are merrily moving along a route in Driver mode when you notice a problem, such as a tree that has somehow planted itself in the middle of the track. You use the UDS to jump into Surveyor mode to fix the problem and then you save before continuing in Driver mode. It took me a little while to realise that when I save it should be the route only and not the session. If you save the session then the consist will be saved in its current position, not where it started at the beginning of the session. So when you restart the session the consist is not in its correct starting position but is somewhere down the track.