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There could be a few reasons why you are only able to authenticate with the pre-built Authentication-Users table in Firebase's signInWithEmailAndPW instead of your own custom real-time user table:

1. Incorrect configuration: You may not have set up your custom user table correctly in Firebase Authentication. Ensure that you have set the custom user table as the default authentication database in Firebase console.

2. Authorization rules: If you have defined authorization rules in your database security rules, they could be blocking access to your custom user table. Make sure you have set read and write permissions for your custom user table.

3. Incorrect code implementation: Check to see if you are using the correct code implementations in your app. Ensure that you are using the correct method for authenticating users against your custom user table.

4. Data inconsistencies: Check for data inconsistencies in your custom user table. You may not be able to authenticate if there are issues with the data in your custom user table.

5. Firebase limitations: It's possible that Firebase may have limitations on custom user tables or that there may be some features that only work with the pre-built Authentication-Users table.