hmmm...the problem is only half fixed.
If my session begins with an auto-login then all the levels are reset to zero. However, if I login manually via the login screen then it loads the previous mixer settings from when I last shut the computer down.
I tried auto-login with a 1 second wait to choose another user before auto logging in, so the login screen is briefly displayed... It works with that setting and loads the last mixer settings
Any ideas why this could be. It's not really a big issue now since the auto-login with small interval to choose another user works, but it seems a bit odd?