Hi Peter.
The psysical Controller and controller settings do not have a bearing on what windows can see in this case.
Using MBR, the maximum usable partition size is 2TB per physical disk, no matter how many partitons you create, only 2TB of this is visible to the Operating system.
Since Windows sees the 8TB RAID 5 array as a "single disk", and has been partitoned to 2TB for OS / data and there is 4TB you cannot use, it's a reasonable assumption that you are using MBR to partition the disk.
Perhaps this will help:
http://msdn.microsoft.com/en-us/windows/hardware/gg463525.aspx
HTH
Cheers
Leon