I can’t believe this happened and cannot explain it, but I booted my HP N40L Microserver and installed Windows 2008 R2 x64 onto the first drive. I left the other 3 x 2Tb drives installed.
Thought it was odd that no 100mb space was made on the first drive. Turns out it was put on one of the 2Tb drives. How stupid is that for the installer to do that.
So to overcome this issue, I pulled out all drives except for the one I am installing on. That will now force the installer to put that 100mb on the start of the first drive which is going to be used for the operating system drive.