I have been using David Coppit's "category sort" plugin with no problem. Yesterday I installed Steve Smith's "FeedBurner feed replacement," and in order to make it work I had to change from default permalinks to numeric permalinks. When I did this, several of my categories disappeared from the live site. They are still in the "write post" screen and there are posts that are still tagged with the categories (and if you click on the category name the correct page comes up), but they're just not showing up in the sidebar.
I disabled the FeedBurner plug in and the categories came back. I reenabled it and they disappeared. Did the same thing with the categories plug in - same thing. So it looks like either there is a conflict between these two plugins, or else there is a problem with permalinks and the category sort plug in.
Any advice? If you look at my blog now (http://www.lklawless.com/blog), all the cat's are there because I currently have the category sort plug in disabled.