Try running "hdparm -Tt /dev/sda" replace /dev/sda with the device name for your hard disks. After running that post back here with the results.
You can also install sysstat and use the sar command to see if your system is indeed spening a lot of time waiting on disk reads and writes.
and for bonus points, from that same sysstat package...
iostat -x 5
during a highly disk intensive session. Ignore the first sample output, thats average since boot, the 3 means sample every 5 seconds. this prints a wealth of useful information on the state of disk IO on a per drive basis.
btw, a rather useful performance tool for linux systems -> http://www-128.ibm.com/developerworks/aix/library/au-analyze_aix/index.html
(originally for AIX, its been ported to Linux... catch-22, its output is best processed by an Excel spreadsheet to product graphs... but you can use it on its own.)