Navigation Menus not Archiving Correctly on Site Backup

[Details]
I work on a networked, multisite version of a WordPress installation with about 500 active sub-sites. In order to do maintenance I have a test server. A script is set up to tar and compress the web tree hierarchy, as well as backup the mysql database and move both to the test server.

One of the things that I am noticing is that any of the sites that have custom menus do not get archived and replicated to the test server correctly.

Specifically there is a “Menu Settings” collection of check boxes which appears under the GUI menu organizer from the Dashboard’s Appearance menu. There is one checkbox labeled “Top primary menu” in this area. On the production server this causes the custom menu to server as a navigation menu. On the test server, all of the details of this menu get archived and moved over, with the exception of this checkbox status.

On the test server, this “Top primary menu” checkbox is not checked, and the menu on the resulting site usually reverts to having items for all of the pages created on the site.

The scripted process looks something like this:
[production server]

$host mysqldump --defaults-file=/file/path/credentials.cnf --all-databases > /path/backups/$(hostname)$(date +.%Y%m%d%H%M).sql
$host gzip /path/backups/*.sql

[test server]

$testHost scp user@host:/path/backups/latest.sql.tar /testHostPath/latest.sql.tar
$testHost gunzip latest.sql.tar
$testHost sed -i "s/production_url/test_url/g" latest.sql
$testHost mysql --defaults-file=/path/credentials.cnf < /testHostPath/latest.sql

[Question]
Why isn’t the characteristics of the menu being stored in the database? Is anyone else seeing this on restored or moved sites after exporting the mysql database?