Wubi don't replace the Windows bootloaders. It simply addes an entry for
Ubuntu to it.
The first choice you mention is Grub that was installed when you installed 9.04.
The secound step is the windows nt bootloader, it sound like wubi didn't
properly removed ubuntu from the boot.ini file on C:, could you please post the
content of this file (it's a hidden file).
Also look for any other left owers of the grub and ubuntu files and
folders directly on C:
** Also affects: wubi
Importance: Undecided
Status: New
** Changed in: ubuntu
Status: New => Invalid
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Uninstall of Wubi.exe doesn't restore Windows XP SP3 boot sector
https://bugs.launchpad.net/bugs/464209
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