Online check-in has some glitches. One they've told me about is linked reservations--if you have linked any days, then there's a good chance online check-in won't work on the reservation(s) that have linked days.
I haven't heard about problems with two rooms, tho--I did a trip in May where online check-in worked fine for one villa that had no linked days, but the other villa, which did have linked days (due to waitlist coming through) did not work with online check-in.
The good news is that there was no problem w/the reservation once I arrived, and both MS and Disney tech told me ahead of time that the problem was with the system.
Good luck!