|Check that their cables are in good condition and tightly connected. It's possible one of the drives is going bad and causing both to sporadically not be seen.|
Are they on the same data cable? If so, check their jumpers.
If they're on an 80-wire cable the hard drive should be jumpered Master and connected on the black connector and the DVD as slave on the gray connector.
Or they should have the same black--gray connections but both be jumpered as Cable Select (CS).
If the hard drive is a Western Digital jumper it as Single--not Master--and the DVD as slave. The Single setting for a WD is no jumper.
You're not really green until you're soylent green.