OK, now that I know you have a problem you suspect is drive related:
- Review /var/log/messages* for any kernel messages regarding drive errors: timeounts, "soft" errors, etc.
- Install smartmontools and request information from the drive's electronics on possible problems or errors. See http://en.wikipedia.org/wiki/S.M.A.R.T. and then use smartmontool's smartctl(8) with the -a option to get a complete report on the suspect drive from the on-board electronics.
I started to write a long treatise on hard drives and then stopped. Let's see what you can learn about the drive with this much information.