In the course of making that page, I was surprised to discover that most of my original research seemed pretty much correct. There were, however, some common radicals whose orders needed to be reworked. The most common were 方/万 and 女. I posted to the forum on 12/2/2011 with an overview of all the changes. After I didn't hear a peep about the changes, I went ahead and modified the character database.
Fast forward eight months and significant controversy has formed around the 方/万 stroke order change in particular. The conflict has to do with the order of the last 2 strokes, should it be the hooked stroke first or the cutting stroke? All of my sources said that the hooked stroke should be first, but stroke order in China is not as universally accepted as in places like Japan, and so there is honest room for contention. For this particular radical, the case for leniency is particularly hard to pass up because the two strokes are adjacent and it is easy for us to indicate the two should be written with interchangeable stroke order.
I had resisted making the change out of stubbornness, but after speaking with Nick and Scott have decided that it would be pig-headed not to allow both orders. So, as of this evening (6/25/2012), the following characters should allow any ordering of the last two strokes in the 方/万 radicals. Here is a list of the characters that we support on the site that have been changed, if you spot any additional characters, please let me know via the contact forms on the study page or via the feedback form in the iOS app!