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.
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.