Thought I'd share this in case anyone might benefit...

I had Ubuntu 8.04 LTS Desktop installed on my work machine, but as I don't "own"
the machine & so can't configure the partitions, so I had installed it using the
wubi installer under Windows. I now wanted to upgrade to 9.04.

1) You can't. See the documentation in the Wubi guide. 8.04 to 8.10 or 9.04 is
not supported. The fix (work-around) is therefore to backup your data,
un-install the old version and reinstall the new version.

2) On reinstalling a fresh install (still using the wubi-installer) it would not
find the Ubuntu installation when I got to the re-boot stage. This is because on
my machine it did not update the boot.ini. (It might be something to do with the
fact that my Ubuntu is on D:, not C:)
To fix this I had to add a line to the "[operating systems]" section of boot.ini
as follows:
C:\wubildr.mbr="Ubuntu"
Note that it is c:\, even although my Ubuntu installation is on d:\