I also had the screen off center problem with the 3.0 & 3.1 Defender firmware after system repower. I tested a few SNES games and I couldn't detect any performace improvements, myself, so I don't think there's any loss in going back to the custom firmware. I did flash back and forth several times with no bricking on my unit.
Secret of Mana performs really awfully on the Letcool... bummer!