Try manually mounting the drive using Drive Setup. If that works, try updating the driver and rebuilding the desktop. That usually clears up the problem. If it mounts manually, but doesn't want to mount automatically and these didn't fix it, it is probably spinup latency - the drive is not spinning up in time to be seen when mount check is run. You did not say what OS level you are at, but OS 8.6 and 9 do a second mount check when the desktop is started. You may be able to go to one of those to fix that.
If you can't manually mount the drive, or none of the above works, check the drive and cable. If the cable has ANY cracks or splits in it, replace it. If not, reseat both ends. Verify Master/Slave setting. If the drive has a jumper for "over 8GB translation", which many do, make sure it is off. As a last go, start the machine while open, with your hand on the drive. Feel its spinup. If you do not get a smooth motion, the drive is bad.