I've only found it does that when you scroll up from the bottom manually - it'll stay with the text you scrolled to. Quite a nice feature, since you obviously scrolled there to have a look at that particular part, so it'd be annoying if subsequent writes to the log bumped you away. Just press cmd-down arrow to go back to the bottom where it'll scroll along with new writes.
If this isn't what's happening, then try cmd-k to clear it and see if it starts 'working' again.