This question has been answered by leoandrews. See the first response.
<base href="[[!++site_url]]" />
Do you know how the routing was being done (iow, how were users directed to the correct site)?
Make sure you have an uncached (with the exclamation point) site_url tag in the head section of all templates:
<base href="[[!++site_url]]">
/* Initialize the default 'web' context */
$modx->initialize('web');
/* setup for multiple domains */
switch(strtolower(MODX_HTTP_HOST)) {
case 'www.myothersite.com:80':
case 'myothersite.com:80':
case 'myothersite.com':
case 'www.myothersite.com':
// if the http_host is myothersite.com switch the context to the other site
$modx->initialize('web2');
break;
default:
// by default / if no other rule can be applied, load 'web' context
$modx->initialize('web');
break;
}