My account is with Etrade. I have experienced the problem you have have mentioned in the past. My KFT share cost basis is also not automatically entered by Etrade into my Portfolio view. In the past when I called them about this problem, they told me that the Portfolio is not the "official record" and is provided just as a service to the customers.
The bottomline is that you have to routinely check to make sure that the information is correct on the Portfolio view and manually edit that yourself.