Secondary Hard Drive being lost when primary is busy.

Folks, I have a strange problem which has gradually been getting worse over the past couple of months. I have a system which I built with a primary SSD containing the OS and a secondary 1Tb WD caviar green drive which contains mostly media files. The second drive is partitioned into 650mb, 250mb and 100mb partitions. The problem started to show up a couple of months ago when the partitions...