I've been struggling with MT, along the lines of the previously reported missing category problem. It had become impossible for me in the past week to post anything using NetNewsWire without getting a time out and the dreadful wrong URL that gets spilled everywhere through pings and RSS files.
Pings! Here are the culprits. Following advices here and there, I added Technorati, bloggrolling and weblogues.com to my ping list about a week ago. Wrong move. Pinging those sites, or one of them, adds a significant delay to the build process, hence the consistent time out with NNW. All of those sites (apart weblogues.com but that one is for French weblogs) will pick up my updates through the default blo.gs and weblogs.com anyway.
Lesson: always note changes you make to your MT configuration. I knew it, I just have a terrible memory :(.