We have finally got to the bottom of this. The Master Module is needing to see a session with saved S6 data in it before it will save out again. So if you are a new S6 user there is no way this would have worked (I have provided a PT session with saved data below). If you had this working in earlier S6 versions then the workaround for now is to load an old session(or the one below) that does have the S6 data in it, then close it, all sessions from here on will save the data correctly....until the Master Module is rebooted. Once your session has this data it will save correctly without having to do this load/save.
One way is to make a template with saved data working and always make new sessions from that.
We are working on a more permanent fix.
Blank session with S6 data