cliconfg.exe should be the x64 version. I've been using it (even it's an old tool) and it created the aliases under the x64 "SQL Native Client 10.0 Configuration". Ok.

Are both instances using same port or you've put different ports?

Concretely on my environment with two instances I use different ports for sql 2008 and sql 2012, and I have enabled the ports via the Firewall.

Regards,

IgorMi