well there is nothing wrong with the database class file, it has been untouched since Mys v1.3.1 and it still works the same way in Mys v1.3.3. Did you check from phpmyadmin whether the table prefix_settings has the necessary entries? It may be present but is actually an empty table?
Anyway, what error message do you get exactly on your site? Also you may want to check your config.php file to see if anything is abnormal from there. I wont be surprised if your host does not really understand the situation at all.
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