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It sounds like you are doing the right things. I wonder if perhaps there has been a regression with the database upgrade code in recent Sneaky Peek releases? Try grabbing one of the older releases in the Sneaky Peek directory and see if it does any better at converting your database. When you start up 1.1 with a 1.0.3 database, you should get some ominous warnings about converting your database.

Okay, I did some testing, and found that if you go back to the 104954 release, it should work properly. I'll file a bug report.