I'm used to testing hard drive transfer rate with HDTune. Generally, a good drive will start somewhere around 100MB/s and decay downward during the test to perhaps 50-60 MB/s indicated - with a somewhat "noisy" plot of measurements.
Bad hard drives will show periods of time where the transfer rate drops to very low numbers, i.e. 1-2MB/s and will stay there for 10% or more of the time.
I'm working on one right now that was staying low for fairly long periods of time during the test and replaced the hard drive and SATA cable and the SATA port on the Mobo. I have never experienced this in such a repair evolution.
Yet, it appears that the variation to very low numbers persists at least somewhat. So, I'm wondering:
What if these efforts didnt' fix the root cause of the problem?
I'm running a CHKDSK right now but rather doubt that could affect HDTune.
What if the problem remains? Where would you be looking to fix it?