I have installed Windows Server 2008 Standard/Enterprise/Server Core/Data Center several times on this board without any problem.
Actually, using the Intel Matrix Controller, the Windows Vista/2008/Seven have the F6 raid controller driver embedded in the Operating System.
So there is no need to embed the driver as the drive should be automatically recognised, and thus allowing you to do the installation of the OS.
Actually, after installing the OS, i used to install the Intel Storage Matrix Manager as it installed the Intel Raid Driver.
I remember to get problem installing Windows 2008 & Windows Vista only when using an OEM version of the Windows. Actually, it could not find the drives and it does not load the Intel F6 Driver, it gives an error message, Contact your vendor ...
When using a non-OEM version, it works perfectly fine, so i will say probably, this can be your case as well.
Let me know how it goes.
I´m not sure qhy you want to use the Intel Raid mode. We only use the LSI mode because than you can use the raid web console to manage the array and, much more important in my eyes, the raid controller manager is enabled to send you mails in the case of raid problems.
This is an important feature which is missing in the current release of the Intel Manager so we don´t use it in server environments.