Hi Ken,
unfortunately I think that the 512e might really be an issue - when you are performing writes and your I/O requests get segmented (because of a misalignment) you get a performance deterioration - more so when it's "just" 7,2k RPM drives in RAID1 - could you try getting disk(s) with native 512 sector format, doing a storage vMotion there and compare the performance?
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