Steve try to do a recompile of the code before you ever open it up to have the scripts run. Then run it on a clean DB. I think this may have something to do with running this on 1.1 when it was built with 1.0. I've successfully run the upgrade and a new install on 1.1, but that does not mean you have a little something different in your install. I assume you have either the aspnet user or the Network Service in 1.1 set up for full permissions on the file folder DNN resides in, right?
Also there is a verison table that will tell you the last script to run. That information will be helpful in trying to determine what the cause of this may be. You should also have a log file showing any error encountered in the script runs in the database folder.
Bruce