Ok, I don't know WHDload extremely well, other than using it successfully for my games.
A
couple of
searches gives plenty of topics to review though.
At least you were correct to reinstall everything if the maxtransfer setting was wrong in prolonged use, as files would be corrupted.
Off the top of my head, if you don't know if it is hardware, your wb setup, or your whdload setup that is to blame, you could always run checks with a plain 3.1 install, other whdload versions, the same setup in winuae, on other amiga hardware, etc..