Hi,
I have about 200 categories which are all of the municipalities in Sweden. Of some reason not all of my categories are ordered alphabetically. The first 21 items in the list are just random ones, and then the rest is ordered as they should. They are all child categories of a category called "Municipality".
http://i44.tinypic.com/4qq89l.png
I've tried running it on TwentyTwelve with all plugins deactivated, same result.
Thanks.