Hey. I have windows and I popped in my ubuntu disk, and hit the "Install inside of Windows" option (I installed it on my secondary hard drive). It installed, then I booted into linux, and it created the image etc. After that, with high hopes, I went to boot into linux to start using it. I got the following error:
"Booting 'Ubuntu 8.04, kernel 2.6.24-16-generic (recovery mode)'
Filesystem type is ntfs, partition type 0x7
kernel /boot/vmlinuz-2.6.24-16-generic root=UUID1030B50730B4F4B6 loop=/ubuntu/disks/root.disk ro single

Error 15: File not found

Press any key to continue..._

Please help!

reinstall it....

My first guess would be to check the Windows bootloader parameters.
I am guessing you have Windows on your "primary hard drive" and the "secondary hard drive" is formatted NTFS for extra room. I don't know how well the Wubi installer handles this. May just need some changes to the bootloader.

EDIT: It would be helpful if you would state which Windows version you are using; what hard disks you have installed; and post the output of "bcdedit" (run the Window's command prompt as administrator and type the command).