I think this is also a duplicate of
https://bugs.launchpad.net/ubuntu/+source/lupin/+bug/604417 which is a problem
in the lupin overrides of grub, as it relies on the existence of the file
/host/wubildr to determine if it's a wubi install.
If you don't install wubi on the same partition as windows, then /host/wubildr
does not exist, so it assumes it's a real ubuntu install and uses the real grub
commands, not the lupin override.
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Fresh Wubi 10.04 install + grub update render system unbootable
https://bugs.launchpad.net/bugs/609815
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