I was having a problem with codesigning my apps, so I deleted all the keys from the keychain. Then I went to Certificate Assistant => Request a certificate from a Certif
You are (perhaps accidentally) asking Keychain Access to generate a Certificate Signing Request using an existing key. If a key is selected when you go into the Keychain Access - Certificate Assistant menu, the options presented will be for that selected key.
Choose a non-key item in your keychain (like a saved password) and go to Keychain Access - Certificate Assistant again to generate the CSR normally.