I've installed Windows 7 over a dozen times and this has never happened before. I finally got a SSD Drive and installed Windows 7 on it but instead of creating the 100MB system partition it installed it onto one of my other hard drives which I now need to erase. Can I change the system boot drive to another hard drive or partition? It would be a big pain to re-reinstall windows even at this point.
So I had to reinstall Windows, Oh well. but you can still avoid this problem if you have multiple hard drives if you delete the main hard drives you want to use volume then create a new volume (it will pop up saying windows might use space etc.) and it will create the 100MB system partition on the same disk, if you just delete the volume and click next it will install it on the next available hard drive.