Settings not saved

I saved a project that included several instances of Mystic plus some 3rd party plugins. When the project was reopened all the settings in all the instances of Mystic were lost. Some midi notes were very faint and others very loud. The result was an unbareable racket on all instaces of Mystic. Some crackling also developed. All 3rd party plugins were unafected. When loading another preset into Mystic and then reload the old one back, it goes back to normal. ie, how I originally saved it so, hopefully I havent lost my work but I am reluctant to continue on the project while it is so unstable. I am so close to completing the best thing Ive done on Cubase since I started several years ago so I saved several backups for fear of losing weeks of work but they are all suffering in the same way.
This morning I lost the sound completely afer side chain ducking a track caused C6 to crash. I say crashed, everything seemed to work normally but with no sound.
I installed the latest update for Cubase 6 yesterday, could this be causing the problem or should I re-install it.
Thanks in advance