Hard drive passes all tests but extremely high response times causing major performance issues.

I have a HP Compaq Presario CQ62-360TX pre-loaded with Windows 7 home premium (64-bit) that I purchased just under a year ago.
Recently my experience has been interrupted by stuttering that ranges from annoying in general use to a major headache when playing music or videos from the hard drive.
The problem appears to be being caused by extremely hard drive high response times (up to 10 seconds).  As far as I know I didn't install anything that might have caused the problems before this happened, and I can't find anything of note looking back through event viewer.
In response to this I've run multiple hard drive scans for problems (chkdsk, scandsk, test through BIOS, test through HP software and others) all of which have passed with no problems. The only thing of any note is a caution on crystaldiskinfo due to the reallocated sector count but as none of the other tests have reported bad sectors I'm unsure as to whether this is causing the problem. I've also updated drivers for my Intel 5 Series 4 Port SATA AHCI Controller from the Intel website and my BIOS from HP as well as various other drivers (sound, video etc), as far as I can tell there are none available for my hard drive directly. I've also wanted to mess with the hard drive settings in the BIOS but it appears those options are not available to me even in the latest version.
System Specs:
Processor: Intel(R) Pentium(R) CPU P6100 @ 2.00GHz (2 CPUs), ~2.0GHz
Memory: 2048MB RAM
Video Card: ATI Mobility Radeon HD 5400 Series
Sound Card: ASUS Xonar U3 Audio Device or Realtek High Definition Audio (both have problem)
Hard Drive: Toshiba MK5065GSK
Any ideas?
 Edit: The drive is nowhere near full, it's not badly fragmented and as far as I can tell there's no virus or malware.

Sounds like failing sectors are being replaced with good spares sucessfully so far, this is done on the fly and will not show in any test, you have a failing drive, I would back up your data and replace the hard drive.
Sector replacement on the fly explains the poor performance also, replacing sectors with spares is normal if it is just a few over many years, but crystal is warning you there are too many, a sign of drive failure is around the corner.

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