I had the very same issue with my Galaxy Y Duos. Rotating the phone or laptop screen through screen preferences didn't help me. Finally the solution was to use 'Flip This' chrome extension and rotate the QR code by 90 degrees. The WhatsApp logo at the center of the QR code would not change its orientation on the camera (as it is a different image) but the QR code would be rotated and your phone would be able to scan it.