I figured out what was wrong - and thought I'd update this post in case anyone else sees thi sproblem.
My problem was just with the one project file. I tried a new file and it was OK, and then I checked my template (and deployed a new project from the template) and that was OK too.
The one file seemed to have a problem where the "Notes" became read-only. Changes were not saved, and I even deleted the entire notes section (including Name, artist and album) - and when I saved and re-opened the file, the original notes were still there!
I reverted back to the 2016.10 update, opened the file - and deleted all the notes.
Then I updated to 2016.11 again, and now the file works OK.
- Remember to save your original Notes out to a text file - if you try this.
- I had to set up my synth rack etc again in the file - but that's not difficult.
- all my other files (which weren't touched when I went back to 2016.10) were fine and didn't need to be set up for synth rack settings etc.