Until now I had a very easy life with my backups by using GUID partition tabled disks only. That applied to OS X and Windows. Unfortunately all SATA cards that I have used so far keep the native Windows partition table MBR which is a mega PITA in my view.
It comes back to how the GUID was done on each OS. It's not the same, and why they're not compatible, not just the filesystem. (Windows GUID /= OS X GUID. This is what I was talking about with the offsets).
You've been working with the low level areas, and that's where they seem to be mortal enemies.

If you keep to the higher level (file systems), you can get them to work with one another, albiet via a 3rd party application for full access (read + write).
MBR cloning works with Acronis which is bloated and costs money. The logistics of maintaining different drives with incompatible partition tables are as pleasant as having someone piss into your beer. If I had known what I was in for I had never attempted it.
I don't know what it costs there, but I managed to find it for $30USD. Cheap for paid software that actually works these days.
It does do a neat trick though, and you may not have tried it. Instead of a clone, just make a full backup of the Windows installation with Acronis (it makes a copy of the MBR, unless you elect not to. Don't do that). Burn the boot disk for Acronis. You can then reinstall that backup to a clean disk/array using the Acronis boot disk you just burned. I've done this, and it works for both Windows and Linux, as it can read/write the different file systems. IIRC, it does work on the trial version of the software. I know for certain it does for me in the full version.
This can help reduce the need for multiple disks for backups, though it must be so for clones. NAS is even better, as the file system is a non issue. Again though, clones are the exception.
I had a perfectly good Windows drive with high performance AHCI SATA driver, all devices properly fitted with drivers to Bootcamp 3.0 level. All updates done and all the apps and utilities loaded which you already have in OS X but need in Windows and all that on Vista 64. Just to do this RAID thing I had to start from scratch to install Windows on a single MBR partitioned drive. Did all the updates, all the drivers, all the apps again, configure the blimming thing so that I can actually work with it. The master boot record patching and registry editing for AHCI drivers took me 3 hours alone allthough I had it done only some months ago.
Once the array was set up under the ARC-1210 (it will be MBR), you plop in the Windows disk, and go. During installation you will have to select Load Driver, install it, select Refresh, then select the array. Format to NTFS, and proceed with the installation.
Its no more complicated than that for a clean installation. Then you have to do the rest of the associated bits with Windows (updates & drivers).
Now I have to figure out how to clone my single MBR partition tabled drive to my RAID0 array. My first attemp went wrong. I managed to clone the thing but it isn't running. The partition is active but it isn't shown as the system drive.
How the hack do I get the cloned drive to actually boot?
Could you give some specifics?
i.e. MBR, GUID partition, what it was set up under, what's trying to access it (say an OS X clone util attempting to access a Windows disk as an example),...
It could really help, as I'm now a little lost as to exactly what you've done on this incarnation.
