Originally Posted by stress_junkie
I believe that the first partition has got to be a Windows system partition. I'm not sure about that.
Also, it is not unusual for a disk that was partitioned under open source software to have compatibility problems with Windows.
The best course of action is to install Windows then install Linux.
You should be able to get Windows installer to recognize the disk if you zero out the MBR. For example if the disk is /dev/sda then you could open a terminal window under the root account and enter the following command.
dd if=/dev/zero of=/dev/sda bs=512 count=1
There are numerous discussions on this subject at this web site. Use the web site search feature to look for keywords such as "windows install".
When giving this kind of advice it always a good idea to warn about the consequences. This command will erase the whole MBR, including *also* the partition table, which means that no OS will be able to see your partitions until you recreate them. The data will be intact, but you will not be able to access it via your OS normally. Testdisk can fix this, amongst many other problems.
If you want to zero out everything *but* the partition table, use this instead:
dd if=/dev/zero of=/dev/sda bs=446 count=1
This will erase the bootloader, which means that you will not be able to boot unless you reinstall it. Installing windows will provide you with the windows bootloader, which will allow you to boot windows. Linux will still be installed but you won't be able to see or boot it. You would need to reinstall grub or lilo (whatever your distribution uses) before you are able to boot it.
Both can be configured easily to boot windows as well.
It's true that windows is a complete moron when it comes with dealing with other OSes. It's part of their policy that Windows is the only OS you will never need. So there's no need to make it interact in a friendly way with the rest.
That's why, in general, and if you don't want to bother, the easiest thing is to install windows, then linux. Most linux installers will add your existing windows partition to the bootloader for you.