When i complete the first journey it ask me if i would like to continue the journey it doesn't it brings me back to where i started intially, its like i hit restart, is this normal.
Is it restarting the California Commuter Scenario? If so thats odd, but you can select the next journey if you go to: Journeys->Peninsula Corridor Journey->Chapter 1 and there selecting the next entry under the ticked one. For me the next journey function works. There are just a couple of Services in the list aswell which look pretty similar as they all start in San Fran and go to San Jose