I have checked the train timetable for late september from St Pierre des Corps in the Loire to Avignon on the Bahn site (faster travel time than with SNCF)however it says 'subject to compulsory reservation' then ' not bookable via internet'. Can anyone give me more information on this? Has anyone done this train route before?

The Bahn site is the German train site. It is typically easier to use when you are looking up information but if you need to book a ticket for a trip that is not in Germany, you will need to use the train site for that country. You will need to use SNCF site to book on the internet for your trip in France. Take a look at the Buying Train Tickets Online thread for some tips on using the SCNF.

I also would rely on the travel times on the sncf site rather than the Bahn site. They don't have their own rail system on these routes, so if there are differences, I think the SNCF schedules would be the ones you'd want to rely on.

Also, take a look at this current thread for more info about booking through sncf.