Are you sure you've done the following:
Routing Domain to Specific Folder on the Server
Similar to our earlier approach, we’ll be using .htaccess directives to tell the server what the root folder should be for each domain. Last time, we set it so that it would automatically map to a folder based on the subdomain that was used to access the site. This time around, we won’t use that approach because we can’t guarantee that some things won’t get confusing on the server once all domain names are in place. That said, we’ll want to type the directives manually so that we have ultimate control over what folder names go with each domain.
Open your ROOT FOLDER’S .htaccess file and paste the following:
#MAP TLD TO CUSTOM SUBDIRECTORY
RewriteCond $1 !^foldername/
RewriteCond %{HTTP_HOST} ^www\.modxdomain2\.com
RewriteRule (.*) /foldername/$1 [L]
Ive used that site many times and have thus far never encountered an error, you need to ensure your domain mapping is correct for the context
I would check all of your HTAcess and Modx Initiliase settings again, as thats usually where i fail
HTH