Since you are familiar with hardware troubleshooting this is
probably silly
to ask so please do not be offended (no, I'm not being sarcastic)
but did
you reset the PMU? Did you reset PRAM? Are there any other devices
connected to the server (FW drives, 2nd ATA card, SCSI card)? If
you reboot
the server with the drive in the bay does it then appear? Does the
drive
spin up with its red light? Does the server recognize the drive
module when
booted to a CD?
These are all good questions. I did zap the PRAM on the machine.
There are three other ATA drives in slots 1-3, and since discovering
the problem, the fourth drive has been replaced with a FireWire
(lacie) drive - but the problem predates the FireWire drive.
If I boot the machine with the drive in place, the drive light stays
red. I have not booted the machine to a CD, since it is a production
machine and I'll need to schedule an outage to take it offline.
Ditto for the PMU reset.
Actually, a question about the PMU - I can find on the Apple website
a link to resetting the G5 Xserve PMU: