Why does my “oninvalid” attribute let the pattern fail?

If you set a value with setCustomValidity() then the field is invalid. That is setting a non-zero length string causes the browser to consider the field invalid. In order to allow for the effects of any other validations you have to clear the custom validity:

<input type="password" name="user_password_new" pattern=".{6,}" required
   oninvalid="setCustomValidity('Minimum length is 6 characters')" 
   oninput="setCustomValidity('')" />