First of all, if you are installing onto a "clean" disk with no valuable data, the worst that it can do is fail to install. If it installs and works, cool, you're good to go. If not, you can try to fix it.
Now, I've found some other people on a mailing list who are apparently puzzled by this same problem. Their solution was, in order to play it safe, they wiped the entire hard disk (using a partition utility) and let the Windows Installer create the partitions in the order it wanted them in. This made the error message go away.
So you have two options:
Try it. If it works, you can forget about the problem. If it breaks, you'll end up doing the next step anyway:
Just wipe the entire disk clean (delete all partitions and/or re-initialize the partition table) using a tool such as Gparted, sysresccd, or a Linux live CD. You might even be able to use a Windows PE environment if you insist on not using non-Microsoft tools.