I don't think this is particularly unexpected. Any new ride is going to have troubles, particularly a ride on which the operations have to be so tightly choreographed as on Millennium Force. The ride is so fast that there is literally no time to waste in operations.
The kinds of problems they have been having, as nearly as I can tell, are the kinds of problems that they could not have dealt with in testing. You never know how a ride's timing will be until you run it with real, live people, and you never know all the quirks of a ride (like under what conditions it won't crest a hill) until you've had a chance to run it for a while in a variety of conditions. Remember, it's been colder in the past week than it was in all the time between when they finished the ride and when they opened it up.
As they get to know the ride, they'll get the bugs worked out. They usually manage to do that eventually. It may take all season before the operating procedure is nailed down and just exactly right, but you know they are going to come to know this ride just like they do all the others. How many here remember the single-train no-empty-seat high-wind operation on Magnum last season? They know that ride well enough to know that it *would* work, even though we all "knew" that it wouldn't. That's because they've had ten years to get to know that ride. With Millennium Force, they haven't yet had ten weeks.
--Dave Althoff, Jr.