I have the same problem. I get a flatbed cover open error message when the ADF cover is closed. I unplugged all the cables to the scanner board and plugged them all back in. Pressing down directly the flatbed sensor switch does not turn off or stop this error message. I cannot use the ADF or the flatbed glass to copy/scan at all.
I wonder if it is a bad scanner board or is it a bad flatbed cover sensor switch?
The previous message was from 2009 so I assume and ask if this particular phantom error had been solved. What was the fix?