Just incase anyone was interested in the resolution to this problem, it appears that the poor drive performance was caused by vibrations from the chassis fans.  After replacing about every component in this system (hard drive, motherboard, SATA cable, memory, and CPU's) to no avail, we discovered that our chassis had a mix of 6.8W and 2.8W fans.  When we corrected this so that all five chassis fans were of the 2.8W variety, our disk performance problems appeared to disappear.

For what it's worth, a quick search produces a few reports of vibrations degrading disk performance. For example:
http://www.dtc.umn.edu/publications/reports/2005_08.pdf
http://etbe.coker.com.au/2009/04/22/vibration-strange-sata-performance/

Finally to quantify the improvement in disk speed, here are the results (showing the average and range) of each test from three runs of bonnie++:
bonnie++ -d /mnt/scratch/test_dab66 -n 0 -s 98304 -f

ORIGINAL FAN CONFIGURATION (two 2.8W and three 6.8W)
Writes AVG = 5348; 4327 - 6369
Rewrites AVG = 2489.5; 2284 - 2695
Reads AVG = 9575.5; 7778 - 11373
Random Seeks AVG = 68.4; 65.3 - 71.5

CORRECT FAN CONFIGURATION (five 2.8W)
Writes AVG = 53901.333; 43143 - 60430
Rewrites AVG = 27684; 20178 - 31942
Reads AVG = 75541.333; 65704 - 80717
Random Seeks AVG = 181.333; 117.9 - 218.6

Many thanks for everyone's time and help.

Sincerely,
Devin