The change to computer-assignment HAS occurred in the last few months. Don't know what day they actually went "live" with the computer-assignment facet of their system upgrades, but I do know all those computer issues during the Fall of 2010 were related to the upgrades that were made to all the reservation systems (if you google search it, I'm sure you can find numerous threads regarding the mess the on-line system, and the phone-in system too, had throughout the Fall...including times when the entire system was down. Usually the phone people could help when the on-line was down, but there were times when they could not "see" information, too. And lengthy delays. And lots of glitches in the various systems and on Disney's various websites. All that seems to be vastly improved now.)
By the way, both times we stayed at POp Century we were given connecting rooms...and we didn't actually want them. We'd prefer not to have that interior door, because we find we hear a lot more noise from the next door room when that inside door is there. But anyway, every time they assign someone to a room with a connecting door, then 2 rooms come out of the connecting-room supply. So I can see how it is completely possible to run out of connecting rooms...if they end up assigning those rooms to people that did not request them.