My family and I were at POP Century 2 weeks ago and all the buses running from the resort to the Parks never stopped at AoA Resort. It was a dedicated bus run for POP, with the exception of the Disney Express from the Airport, which stopped at AoA first.
I'm not sure if the change you're speaking is a new one, but as of September 2012 the POP Century buses were still a dedicated service.
I believe it depends on the time of day. If the resorts are busy enough to have their own bus, they do. If there are only a few people getting on/off, they share. The buses are constantly changing their routes depending on which park/resort needs them the most.