Had this same problem upgrading from 10.04 to 10.10 , while wubi was
installed in D partition and Windows 7 on C.

Symptoms:
Not being to able to boot Ubuntu , while being to boot Windows7 successfully.

Solution:
Copying wubildr, wubildr.cfg, wubildr.mbr from C to D solved the problem 
smoothly.

-- 
grub-pc upgrade renders computer unbootable when Wubi is installed to partition 
other than Windows
https://bugs.launchpad.net/bugs/610898
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