Check your metadata cache. If you're using some external caching mechanism (like Memcached or xcache) it's probably shared across your vhosts. If one vhost populates the cache with its own mapping metadata (after apache restart), second vhost just uses it and doesn't care about different .dcm.xml mappings.
If it's your development server/vhost, it's usually much better to disable ORM caching at all (config/autoload/database.local.php).