Same problem here.

OS: Windows 7 64-Bit
Partitions: 1 System-reserved, 1 C:\, 1 D:\
Tested with: ubuntu-10.10-desktop-amd64.iso

After running the Wubi-Installer and rebooting, the setup-dialog stops at 271% 
and the error message pops up: 
"No root file system is defined.
Please correct this from the partitioning menu"

So I booted the LiveCD and tried to run the installer from there. In the
Live-Environment I can easily access the Windows-Partitions and GParted
shows all the partitions, but when I start the installer, no hard drive
appears in the "Allocate drive space"-dialog. Nevertheless I can choose
"/dev/sda" to install the bootloader on. However when I click on
"Install Now", the error message mentioned above occurs again (No root
file system is defined ....).

fdisk provides additional information: It says that the "System-
reserved"-Partition "does not end on cylinder boundary". (Screenshot
attached)

I tried to access the Wubi-VirtualDisks from Windows to provide the
requested logs using some ext2/ext3-drivers/explorers but without
success. I can attach the logs from the LiveCD, if that helps.

Towards the end of the year I will reinstall Windows 7 and try to
install without the "System-reserved"-Partition and see if that helps.

@thefons: afair Wubi does not support RAID

** Attachment added: "Screenshot-003.png"
   
https://bugs.launchpad.net/wubi/+bug/259540/+attachment/1719393/+files/Screenshot-003.png

-- 
Wubi - "No root file system is defined" error 
https://bugs.launchpad.net/bugs/259540
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