I have found their web self-service portal "My Disney Vacation" to be unreliable as well.
It seems though that when I talk with a CM, the informaton is correct on "their system". Therefore I wouldn't trust the web information.
I originally booked via the web, and when I first had issues with getting wrong information via "My Disney Vacation" I called them on the phone and asked for a written confirmation. Within a few business days I recieved a letter which gave me a detailed, itemized description of what I had booked.
Having that piece of paper gave me peace of mind, and I see that in the big packet I just recieved with my travel documents, I got another copy of that confirmation letter.
Long story short, if you have any doubts, and you are the kind of person who will sweat the details (like me), call them and ask for a written confirmation.