did you book directly through disney or a 3rd party site like expedia or travelocity?
i had the same issue with online check in. i booked through travelocity and had quite the headache. I finally was able to get a phone number for online check in tech support. they told me to try using the site http://www.mydisneyreservation.com and i had to scroll to the bottom of the page and where it asks for how you booked i chose Through a Group or Convention and then was able to complete online check in.
Hope this helps!
We've been getting it the last 4 days. I called Tech Support and they said that because we have a complicated vacation split between 2 reservations, then it won't let us check in online. she said they will fix it but not sure when they will do it. She said that if you go on ME on one reservation and then go back on ME on another then you won't be able to check in online rightnow.