the only thing I can think of is if one/both drives are older drives and their on the same cable. (both on primary, both on secondary) For a long time both DVD-ROMs and CD-RWs liked to be primary on what ever cable they were on. Don't ask me why, I just maitnence them, I don't design them. I have an older DVD-ROM and CD-RW in the same box for awhile and for a while the windows box they were in randomly would decided that the slave didn't exist on boot. A few years later and I replace the DVD-ROM (lense was dieing) and put the new DVD and old CD-RW in my linux box. After awhile I discovered that my DVD-ROM would quit working randomly. At first I thought it might a power problem, but after switching which was slave and which was master (DVD was slave and I used it more than the CD-RW), and since then I've never had to do a hard reboot to use the slave.
Long story short, try switching which is master and which is slave.
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