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Since about windows 2000 Microsoft has added a protection to the Windows installer which will not allow you to install their OS when the drive you want to install to is not the first in the drive array. So as an example lets say I have GNU/Linux installed on my first drive and then a free drive in the second sata slot. The windows installer will not allow you to even operate on the second drive. The installer will come back and tell you that the drive is not formatted properly for windows and will not allow you to format it. Even a brand new and properly formatter NTFS disc is still no go, due to this protection

My solution for the past decade has been to unplug all drives except my intended windows drive and then do install of windows, then making a image of it so I dont have to do this again.

I would though like to know if it is possible to get around this protection?

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I believe this is because the Windows Boot Loader needs to write its NTLDR details to Disk 0, and if the disk is in a non-windows readable file system (you mentioned it's Linux) then it can't write its boot loader, but I'm not 100% sure, so I won't post it as an answer unless someone can verify it – Mark Henderson♦ Jan 8 '10 at 3:12
I agree with Farseeker. It's not a protection mechanism that prevents it. It's the fact that Windows uses a different boot loader and partition type than Linux does. – joeqwerty Jan 8 '10 at 12:28
if you're willing to create a small (10mb) partition on the first drive and let windows use this (almost) as a /boot partition you should be able to install onto the second drive. nasty cludge though :S – MidnighToker Jan 10 '10 at 20:34
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