NetApp Technical Report 3836, "Performance Diagnosis Using Performance Advisor", explains how the diagnose feature works, and what performance counters each diagnostic check looks at. For the LUN mis-align check, it checks the unaligned_reads and unaligned_writes counters. If the version of ONTAP is greater than 7.2.1 AND either of the two counters are greater than zero, then the diagnosis is that the LUN is mis-aligned. A copy of the diagnostic check is shown below.
I'd highly recommend you speak with your assigned NetApp Systems Engineer and you review your configuration. If you're presenting a LUN directly to a virtual machine via RDM, I suspect you need to use that guest O/S as the LUN type, not VMware. The following post is worth a read as it may apply to your situation.
Description: Unaligned I/O requires the filer to read from or write to more blocks than necessary to perform logical I/O. Unaligned I/O might cause an increase in per operation latency. Diagnosis category: SAN specific issues Recommendation: Contact your support engineer. Resource property condition: Storage system should be running DATA ONTAP 7.2.1 or later
Thresholds: Threshold 1: lun:unaligned_reads Default value: 0 Description: Name of the counter
Threshold 2: lun:unaligned_writes Default value: 0 Description: Name of the counter
Algorithm: Existence of unaligned operations when the LUN is receiving I/O indicates misalignment. Remarks: None