Degradation of the disk subsystem performance caused by misaligned partitions is a very old problem. According to Microsoft

This issue may occur if the starting location of the partition is not aligned with a stripe unit boundary in the disk partition that is created on the RAID.

A volume cluster may be created over a stripe unit boundary instead of next to the stripe unit boundary. This is because Windows uses a factor of 512 bytes to create volume clusters. This behavior causes a misaligned partition. Two disk groups are accessed when a single volume cluster is updated on a misaligned partition. Windows creates partitions that are based on a predefined number of sectors. The starting location for a disk partition in Windows Server 2003 is either the 32nd or the 64th sector, depending on the information that is presented to the operating system by the mass storage controller.

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