Comment 1 for bug 464209

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: