High response times in HDD. MFT, fragmentation or even halted disk?

Question

I am experiencing really high response times im my HDD, which can go around 13000ms (from Win8 Task Manager). This occurs when starting up windows and for at least 3-4 minutes, also when doing extensive copy (lots of files). The average read/write speed during that time is around 50Mb/s (total). This behavior started after the first or second partition resize (see below), before that the disk was going really fast.

My Win8 partition is 50% full and recently defragged. The partition had been resized 4 times, from 40Gb to 100, to 350 and to 600Gb (I deleted other partitions). Now, the whole drive only has this one partition.

The HDD drivers are the ones windows downloaded and the SMART status is healthy. Disk is Sata3 in RAID disk controller mode (single drive) and is the WD wd6400aars.

After my little research below (which showed more problems) I can't tell if the disk is halted in any way, if the MFT is fragmented or positioned at the wrong place or if there is something else going on here.

My little research

Benchmarking

Turns out really good using ATTO Disk Benchmark, but...

but in Crystal DiskMark during the last 4 benchmarks I have 0.5 to 1 Mb/s and average response times around 15000ms (cannot be seen here)

Windows Resource Monitor

During startup the windows resource monitor utility showed that MFT had the highest response times (around 8000ms) between all files being used during that time, no matter which process was accessing it. Note that no heavy application runs during startup, besides basic stuff like skype, dropbox etc.

Fragmentation

After the last partition resize, I defragged using Defraggler and the windows utility 2 times. This took some 5 hours each time and since the problem still remains I installed Perfect Disk which revealed two strange issues:

• Defraggler finds the MFT in the middle of the partition and Perfect disk at the beginning of the drive.
• The most fragmented files are the last two files copied to the disk. The Perfect Disk itself. How can this be true, it was just copied into a disk with lots of free space!

Defraggler

Perfect Disk

(bigger image here)

Answer 1

There may be a partition alignment problem with your hard drive. Your WD6400AARS is an Advanced Media Format drive that uses 4K sector sizes. If your OS partition is not properly aligned on this 4K boundary it will lead to much slower than expected disk drive performance due to a process of translation the drive must perform.

Western Digital offers for free WD Align Windows utility on the WD6400AARS Support Page to correct this issue. The utility will analyze your disk and report whether you have a misaligned partition and offer to correct it if so. While this is supposed to be a non-destructive operation, you should back up your data before running this utility.

This Western Digital support page describes the Alignment Tool's functionality in even more depth.

Answer 2

You might want to try defragmenting system files like the page file and MFT at boot time. Defraggler offers this option; it will run when you reboot your computer, on a text-mode screen before the Windows lock screen comes up. You can access this functionality under Boot Time Defrag in the Settings menu. I've done this before and it successfully defragmented the MFT.

Running Windows command-line defrag with the undocumented /b option, which optimizes for boot speed, may also help.