If you've had trouble upgrading to the latest version of Anki, don't panic! A backup was taken of your local deck and the server deck, and any problems you've encountered can be fixed.
Most of the problems have been addressed in 0.9.2, and if you have any further problems, it's likely that your deck had some corruption prior to the upgrade. In the same directory as your deck, you'll find a 'yourdeck.anki-v3' file. If you email that to the Anki author, he will fix any problems for you and send it back.