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The upgrade documentation specifically states to NOT replace the config file ever.
The reason you do not have id's that high is because you replaced the config file with a new version that does not have certain variables. On of those variables is needed to trigger a set of queries that get inserted.
As it is stated in this thread I believe edit your config-inc.php file and place in it at the bottom before the closing ?> this $onthefly="0";
Then rerun the upgrade.php script and select upgrade 482
The queries will be inserted and then you can manually change the variables.
Basically in an upgrade the program assumes you have the proper cookie variables inserted into the config file and transfers those to the database settings table so you can login to admin or in a new install you enter the correct cookie settings.
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