A HA!
Turns out that in the index.php file, we have this code:
/*
* --------------------------------------------------------------------
* Multiple Site Manager
* --------------------------------------------------------------------
*
* Uncomment the following variables if you are using the Multiple
* Site Manager: <a href="http://ellislab.com/expressionengine/user-guide/cp/sites">http://ellislab.com/expressionengine/user-guide/cp/sites</a>
*
* Set the Short Name of the site this file will display, the URL of
* this site's admin.php file, and the main URL of the site (without
* index.php)
*
*/
// $assign_to_config['site_name'] = 'domain2_short_name';
// $assign_to_config['cp_url'] = 'http://domain2.com/admin.php';
// $assign_to_config['site_url'] = 'http://domain2.com';
In order to get MSM to work you have to uncomment those last three lines and insert the relevant information. For some reason the installation I’m using is pulling the site_url out of that last line anywhere I have <a > in a template. I deleted the URL from that last line so it reads:
// $assign_to_config['site_url'] = '';
and the sites are working fine. I have no idea why it’s not affecting one of the sites, but it seems to be working at this point. Not sure if it’s a legitimate workaround or a hack, but I’ll see how it goes.