The MDD G4s support cable select. If you set the second drive to slave, then the first one may have still been set to cable select, which would confuse things. You should either set them both to cable select, or properly set one as master and the other as slave.
Also, you can switch the two drives and see what happens. In IDE, the Master device controls the Slave device, so if switching it makes it work, then the one that doesn't work as master is bad.