Suggest to let something like WinDirStat run over that Drive, if you have Folders with more then 100k Files this will kill your performance.
You can also use HPReadData or "vbda -vol C: -out NUL -profile" to measure the raw performance over the whole disk.
With 2k8 and onwards the VSS Option can also play a big role in speed, drops massivly when it has to pause may writers with data on disks that are not related to the current object (f.E. Exchange).