After the image was first created did you repartition/reformat the arrayed pair of drives once the bios setting was changed? I think the image from a single drive is finding some problems on the array!
When seeing an array last year while running the RCs the installation went well by first nuking both drives first and then enabling the bios setting needed at the time. The two drives locked together as one once they were repartitioned and reformatted as one to see a clean install then.
You may end up having to do the exact same there as well while arrays mainly serve best for servers and storage purposes especially if those are the WD Green Power models you have in your specs! Oh yeah I had some fun with 1 500gb model removed from the MyBookl enclosure to use internally when needing an extra drive.
They do well for storage but not OSing! as problems kept appearing for any problems installed mainly since those are the low performance energy savers series not the higher performers you look for to run Windows on.
The pair used for the array however were the SE models on the old case on an older case at the time and synced well together while seeing a clean install from the start. I think that is a big part of the problem you are running into there besides trying to keep things in the ide mode rather then leaning at anything like AHCI.
The one problem I did run into here with that array wasn't geting 7 on but once I went to break the array up it took a bit like one nuked with the other unplugged while the second had to see the first plugged in while being nuked! That's how those two were bonding!