Did you try it in a 2008 model?
I don't doubt that this could be the case on the newer systems (Foxconn afterall...). But I seem to recall dedicated Windows and Linux using the ARC-1680 series on 2008 models (booting off of the array, as well as single boot disks per OS attached to the ICH). It's here in MR somewhere (~2yrs ago I think). But the boards are different ('08 v. '09/10), as is the firmware (my stronger suspicion). Either being a possiblity as to why it could work on system A, and not B.
As per Boot Camp, the GPT partitioning scheme wouldn't work on the RAID card (i.e. offset conflicts), even if you didn't have a problem booting your card on the MP with BIOS.
I have a 2007 Mac Pro which I used for most of the experiments and a 2009 Mac Pro. Both machines represent the fundamental differences in the Apple logic board and EFI design. None of these systems will work with the ARC 1210 card to boot Windows and sleep.
It is unreasonable to use anything but the GUID partition scheme with a Mac Pro. It is Apple's approach to dual booting and deviating from that way would mean to violate the system manufacturers specification. So this will always be my first choice of partition scheme.
In a Mac Pro it is also possible to use a separate drive for Windows with MBR partitioning. This would even allow you to boot from one of the SATA ports. Unfortunately it will not help with installation or booting from an ARC 1210 port. The Windows install disk will not identify any MBR or GUID partitioned drive that is run from an ARC 1210 port. If you simply install the Windows in another non Mac Bios machine and transfer it to the Mac Pro it will not boot from the ARC 1210 port.
The simple truth is that ARECA does no firmware that allows you to run Windows in a Mac Pro from one of the card's ports. You may be able to use the card to run Windows in a Bios machine. I admit that I have no experience with that case. But to tell you the truth I'm not interested in that case because I do not consider a Hackintosh. So the case for me is closed until Areca change their firmware policy and produce something that fits the Mac Pro for booting Windows and sleeps.