From what I'm hearing, this is maintenance issue. If you've been to Disney World in the last year or so, you've probably noticed that the monorail is having some issues. I'm all for fixing those issues and in fact, I can see why the Epcot monorail isn't even all that necessary during evening extra magic hours. It's probably just as easy to take a bus to and from Epcot as it is take the monorail when all is said and done. But one of the benefits of staying on the Magic Kingdom monorail loop is having access to the monorail so you can go to the Magic Kingdom; it's a huge for families with children still in strollers. Right now if you're staying at a monorail resort you can get back to your resort from the Magic Kingdom by one of two ways: Monorail or boat. Those boats are small and, as pointed out by one of this site's readers on Facebook (thanks, Chantel), guests in ECVs or wheelchairs can't use them.
Beginning on July 11 2011, the Epcot monorail service will stop operation 1 hour after regular park closing, and from August 1 2011, the Magic Kingdom monorail will stop operation 1 hour after regular park closing. This means that in both cases, the monorail will not be able to return guests back to their resorts after evening Extra Magic Hours. Guests will instead be transported by bus and boats where available. Morning Extra Magic Hour service has not been affected. All indications are that this is a permanent change.
I imagine that more buses will be added during extra magic hours. Obviously, the resort launches can only handle so much--even on a slow night, the lines for the boats are very long. The ferry to the Ticket and Transportation Center actually has a greater capacity than the monorails, but there are only three of them and while it's a lovely ride, it is somewhat slower.
I'll report back when I hear more news. I'm hoping this is just a rumor or a short-term issue.
UPDATE: I just talked to Disney. This is not a rumor and it's expected to be permanent.
UPDATE #2: Hearing some rumors that other CMs are telling guests it's not permanent. Big rumor about a major refurb at the Polynesian. Could this be related? It's also likely related to the new Grand Floridian DVC. Will keep you posted.