You might have a dead PRAM battery, this can cause erradic behavior. Also, what bay are the drives in. The bay that is located next to the processor heatsink is an ATA/100 bus, you should put the best, fastest, or biggest drives on this ATA channel. The bus under the optical drive is ATA/66, put the smaller/slower drives here. The CD-ROM bus is ATA/33, and may not provide the nessicary bandwith for both drives. Once you try arranging the drives like this, it may become more stable, and reliable. If you still do not have success, try reinstalling the operating system, or making sure you have the latest firmware (MDD Firmware 4.4.8).