The problem is not only that the drive and motherboard are cryptographically married. There seem to be a lot of checks being made between drive and motherboard, that will cause your console to not being able to update if you have a replaced drive. The last update in spring 2011 was specifically made to detect modified drives, and in turn a lot of consoles with swapped out drives would not be able to finish the update, as the altered firmware on the replaced drive was not properly flashable by the update. So essentially, if you want to continue to play the latest games, that require an updated firmware, do NOT attempt a self repair.
If you have a controller plugged in as a USB Device (for example a guitar controller), these controllers will always sign in before the wireless controllers. So check if you have a USB controller or Wireless Headset that occupies the player one segment.