I’m having this issue too. I also later noticed that it ignores posts created by Twitter Tools but I’ve made other posts since then and it hasn’t updated, even after hitting the Update Tweets etc buttons.
I also _had_ supercache but I’ve completely uninstalled it… but it sounds to me like it’s still interfering in the database somehow. I don’t know. Halp?
EDIT: It works! The buttons don’t work apparently, but after 10 minutes the latest non-blog tweet eventually appeared. Whew.