This is a known issue with Google Account Authentication. If you created an application and installed it to use Google accounts for authentication, and you yourself use a Google Apps account, you will not be able to authenticate against your application as an administrator using this account, even if you created a Google account for this email address mail. The workaround for now is to create a gmail account and add it as the administrator of your application, using this when you need to authenticate against your application as an administrator. You can still use your existing account for deployment and log in to the admin console.
This is a pain, I know - I encounter it every day myself.