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Despite the site_frontpage variable being saved into the domain_conf table for a specific domain, the front page for that domain displays as the site-wide default front page.
Looked at the following:
http://drupal.org/node/1144964 - Nothing in our themes is redirecting or otherwise munging the front page. We've confirmed this by changing other site information for this domain, then visiting the domains front page. None of those changes are displayed. However, if we visit the canonical URL of the front page for the domain in question, those changes to the domain's site information are displaying correctly.
http://drupal.org/node/496670 - Changing the weight of the modules did not work for us as it did for this user.