I’m not sure what was happening, but my .htaccess file was all screwed up and some feeds were not updating. I’m sorry for the confusion, but it looks like an update I applied to Movable Type was causing the problems. For most people this isn’t an issue as the vast majority have already been using correct feed, but check your RSS URLs anyway.
For now I’ve removed all of them except for the following which everyone should use from now on.