Though I would recommend a clean install of Ubuntu along Windows (not with Wubi), I think I have found the solution to your problem.

Hi all,
I had the same problem as the original poster and [SOLVED] it in a very simple way. Here's my story:
I installed Ubuntu 11.04 64-bit using Wubi in Vista and a clean ISO. I got the "Try hd(0,0): NTFS5: No wubildr" error and after a minute or so, Grub loaded and Ubuntu booted. I wanted to find a fix for the wait.

I discovered that my first partition [ hd(0,0) ] is a small (FAT?) partition Windows uses to store it's MBR and a few other things. My second partition [ hd(0,1) ] is my C: drive where Windows lives and where Wubi put Ubuntu.
So, the Windows Boot Loader was looking for "wubildr" on my first partition when really it was on my second partition where Wubi put it.

To correct this, I copied wubildr to the 1st partition. I don't know how to access the 1st partition from Windows, but it can be mounted and accessed easily in a Linux command prompt.

Note: this solution was successful with Ubuntu installations on both the 2nd and 3rd partitions.

and

Here's how I did it (in WIndows 7 though).
I went to control panel and searched the word "partition". A result "Create and format hard disk partition" under Administrative tools will show up.
Click on the "Create and format hard disk partition". The disk management dialogue box will open.
Look below.
You will see "System Reserved", (C, (D and/or any other partition that you might have with their respective letters.
Right click on the "System Reserved", select "Change Drive letters and paths". In the new dialogue box, click "add" and then "OK" on the new dialogue box that appears. You should receive a notification similar to the one when you plug in a pendrive.
Now, go to the directory where you installed Ubuntu/Kubuntu, search for and copy the file wubildr and then paste it in the new partition that should have appeared in My Computer. (Do not do anything else to the new partition as it contains system files and might damage your Windows.)
After that, open disk management again and then remove the drive letter from "System Reserved". (You will get a warning about removing the drive letter bu do it, nothing will happen - at least nothing happened on my computer).
Then restart the computer. Ubuntu/Kubuntu should load normally without the "ntfs no wubildr" message.
P.S do it at your own risk, I am not responsible for any damage that might occur.

From this link

http://ubuntuforums.org/showthread.php?t=798283&page=4&s=1a0baa2cb70576d8aa20c32f5f4b9f99