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Have you opened up the ADF feeder and looked in there for a jam, also?
There may be a switch, sensor switch, or similar, jammed, fouled, or just plain broken, in the manual feed area. Check for that, after removing all paper stock from it, with a flashlight.
After that, you printer may simply be 'broken' (what with the previous fussiness you report about its using the manual feed, which has simply gotten worse perhaps), and in need of either service-repairing or replacing. How old is your printer?
(You might try blowing compressed air into the manual feed slot, if you cannot see into it and verify that it is clean.)
Turn it Off for 1 hour or longer. See if that resets the error. (Also unplug it while it is Off.)
How old is the Brother printer?