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Yes jd you're exactly right. Running the script twice and using the same database details creates two system modules - and the refresh problem as well. Not just system modules, but a number of other records are added, like system blocks, permissions on the blocks, groups...
Did you go through and repair the database records by hand, or just retrieve a backup?
I don't know why the install script isn't exiting when the tables exist. It seems to just continue and do what it can
I could take a look, but I really need to get some of my own work done today too