You can always delete the .htaccess for each root directory, then visit each domain.com/wp-login.php then visit: Dashboard -> Settings -> Permalinks & save changes. (Automatically generates a fresh .htaccess)
OR
login to phpmyadmin for each domain,
check out the database… options table… verify the “siteurl”, and “home” columns. make sure they match the respective domains.
OR
Check the DNS zone template. Could very well be possible DNS conflicts.