Remember Commvault uses DNS with hostnames, etc... you may want to verify that the hostname in each site can be resolved separately in DNS from the Commserve.
Not sure how you have the same hostnames at different sites? Do they have different IP addresses? that would be your key to differentiating the servers apart from each other.
Look to the Commvault Disaster recovery documents for help with having a standby server at another site. Maybe that will help?