Thanks again for all the responses.
grub does now recognise logical ext4 partitions. I removed and recreated the partitions with gparted from the jaunty livecd, which took a while. the latest ubuntu grub was then able to recognise the partitions, and I was then able to install jaunty onto the ext4 partition successfully.
It basically seems like, at the first attempt, the jaunty installer made a mess of creating the extended/logical partitions
Now to get wlan working on 9.04