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Well they are different chipsets so yeah that would cause some problems, at minimum you likely would have had to remove your storage controller drivers from Windows device manager in safe mode before swapping the motherboard.
If you didn't do that then it's run the windows repair option via bootable DVD or swap the old board back in to try and remove drivers from the OS before the swap.
If you were running in IDE or ACHI mode on the old board double check that your running the same mode on the new one.
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