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My HDD is WD 500Gb Black.

When my HDD starts copying is has a high speed of 80-90 MB/S. Following this it keeps slowing down as it is copying until it gets to roughly 13-16MB/S.

When connecting a similar HDD in addition to it it became fast and stayed fast. But when I disconnect the other HDD the problem comes back.

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Please post the Operating System that is performing the copying action. – Moab Mar 25 '11 at 14:50
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And the connection system you're using - PATA, SATA, eSATA, USB, Firewire, etc – Majenko Mar 25 '11 at 15:08

Check your virus scanner, disk cache settings and CPU / MEM / NET / I/O usage for clues.

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