I have the same issue getting @server.domain.com instead of @domain.com. It puts the server domain, not the email host domain. But only on OSX units. IOS works perfect. So I assume its a bugg. You can change it manually in mail.app and it stays there, but it would be nice if anyone know how to fix it.
I reported this to Apple Care today as I am having the same problem with OS X 10.8.2. It was apparently fixed in 10.7 but regressed with 10.8.
It is a known issue and they hope to fix it in a forthcoming issue.
In the meantime as a workaround you can go into Mail app, preferences, accounts and manually edit the email address. I am not sure if this will revert when profiles are pushed out again later though.