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Hard Drive Transfer Rate with HDTune

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?
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dbrunton
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I'd run the manufacturer's diagnostic rather than HDTune in such a situation.  For Seagate it is SeaTools http://www.seagate.com/support/downloads/item/seatools-win-master/ and for WD it is the Data Lifeguard Diagnostic http://support.wdc.com/downloads.aspx?lang=en

That'll give you a much clear picture of the state of the drive's health.
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I suppose it's possible but this is a new hard drive as I'd mentioned.....  I'm looking for other causes.
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jmcg
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maybe both drives came from the same batch?
try another brand to be sure
Is the new drive fresh, without any data on it? What BIOS setting are you using (IDE, AHCI)?

If the data on the new disk is a copy of the data on the old disk, it could be that the test is reading directories and files as one of the tests. If there are many very small files, the performance of the disk is lowered drastically, while large files usually pose no problem.

AHCI should also give you better performance than IDE mode.
So you were running CHKDSK and HDTUNE at the same time?

if so, of course they would interfere with each other!
dbrunton: I have run the WD tests (the old drive installed on another computer)  and they show "OK".

Gerald Connolly: No.  I agree.

Dave Baldwin: "not connected properly in the BIOS" .... how?

All:  Just to avoid the confusion I must have caused.  The problem is with an old drive and it was replaced with a shiny new drive clone.  Seagate to Western Digital.  The new drive showed fairly large transfer rate dropouts as well.  

The system was "stuck" on Windows cumulative update.  i.e. it had failed a number of times.
Once this was done, all is OK.  Well after also running sfc and DISM.
Also, the old drive tests fine with HDTune when installed in another computer.

This is the first time I've seen data rates drop when the HD was OK!!  Noisy numbers but no big dropouts in the rate.
The drive I was having trouble with had a hardware problem that restricted it to the slowest level of IDE connection.  When I put a new drive in the machine, the BIOS was still set for that same connection level.  When I changed it to the highest level, the drive ran normally.  HDtune helped me figure that one out too.
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