Was this true only online, or also in the live broadcast?
The Opening Ceremony shown in the US on Friday was not live. In fact, right at the beginning it said "Previously Recorded." On CNN in the afternoon, they even had an article titled "Chinese president declares Olympics officially open," which is an event that takes place in the Opening Ceremony. China is 12 hrs ahead of the US East Coast. It could not have been shown live, as there were fireworks and darkness throughout the ceremony that daylight would have made impossible.
As far as the order goes, they did mention a couple of times during the television broadcast that the order was not what we were used to, and explained the stroke-number-system that the Chinese organizers were using. It was a bit odd watching, but it made sense to me. Glancing at the list on Wikipedia, I seem to remember the countries being ordered that way. So the TV broadcast and the Wikipedia lists match.
They also briefly showed us the countries that we missed while we were away during the commercial break.
I'm not going to watch the online version, so I can't compare to that. The Parade of Nations is very boring, and I can live until the Winter Olympics in 2010 before seeing it again.
One way to compare the accuracy between the TV broadcast and the online version would be to look at the bottom third graphics. Because of the different order system, they had a dimmed out preview of the next three countries, in a slider that moved along. So, if the online version has those graphics, and the images presented match up with the list shown on Wikipedia, then it is the same version... Yes, I know they could have edited those too, but I'd rather not get out my tin foil hat.
"You need tender loving care once a week - so that I can slap you into shape." - Ellyn Mustard