It is my opinion (n00b though I may be) that:
☼ After installing Windows fresh (which you've done):
☼ Use Partition Wizard 5 Home Edition
(inside of Windows, of course
) to resize the main partition so that you have about 20+gb for the Ubuntu install. Then:
☼ Format the partition (still using Partition Wizard) to ext2 or ext4 (if you don't want to see the Ubuntu partition inside of windows and accidentally write to it and possibly corrupt it, NTFS if you are more alert than that). Then:
☼ You can run the Ubuntu CD/DVD install disc from within windows and install to the new partition you created.
(This should also work on drives secondary to the primary Windows drive).
This is the method I used on my rig, just be sure to have an internet connection hooked to the machine you're using so you can get the Ubuntu updates during the install. Also don't forget to open Terminal once you're finished and run this command to get all of your codecs and extras unlocked (you must be logged in a "ROOT" and have an internet connection):
sudo apt-get install ubuntu-restricted-extras