That also is a good possibility....
My harddrives were cooking a few times and caused alot of errors. I went out and picked up two HD coolers, its just a small heat sink with two fan that blow on the hardrive. Check out coolerguys.com.
If you have the case open and after you shut down, just kinda feel the harddrive and see if its really hot. There are a few software temperature monitors, but I really don't trust them.
There are alot of limitations on cooling based solely on the case. SOme R&D case designers really don't think about airflow too well. I now have a front fan blowing in, hitting the harddrives, and an exhaust (12cm fan just turned around) blowing out the back.
I used to keep the sides of my computer off, but its just a dust magnet then. There has been many of times I just cracked the sides open and put a desk fan blowing right in there. Its not the best things to do, last resort maybe? but it works.
Fans are cheap, but depending one the mother board, you have a limited number of the 3 pin fan connectors. 4 pin are available if you have a few extra power sockets free.
Good luck.
Res