Did you remember to set the jumper so it gets the tick signal from video instead of the psu when you changed to a atx?
check the psu under load at the motherboard connector, its easy to insert multimeter probes in the back of the connector. use any of the blue wires for ground probe.
It sounds like a bad workbench install to me,since you duplicate the problem each time. make sure maxtransfer is set right,although most scsi controllers seem to handle this regardless.
Do all the drives have the same filesystem? ffs,sfs,pfs?
Termination could cause the odd behavior,but hard to say since you have this trouble on multiple drives.