I have a similar issue, not 100% sure if it's exactly the same. My certificate and private key are paired if I look at them in the "my certificates" section of Keychain. Xcode still did not find my identity until I added the build setting "OTHER_CODE_SIGN_FLAGS" to "--keychain $(HOME)/Library/Keychains/login.keychain-db" although the output of "security default-keychain" already points to it.