1) Most likely the IMEI number wasn't updated when the motherboard was swapped. The FOTA server is sending you updates, but its to your old IMEI number. That is my guess on what is happening.
2) Not sure, but I would assume so. We haven't been flooded with complaints about not getting automatic updates, so I would assume this is a pretty uncommon issue.
Get in touch with your local Support, they can help you much more than I can.