qbelmi,
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.
http://communities.netapp.com/message/23935#23935
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
Configuration:
<rule name="LUN Misalignment">
<rule-type>Counter Threshold</rule-type>
<thresh-processing>OR</thresh-processing>
<rule-enabled>true</rule-enabled>
<is-warning>false</is-warning>
<resource-property-conditions>
<resource-property-condition>
<resource-property-name>version</resource-property-name>
<resource-property-processing>gt</resource-property-processing>
<resource-property-value>7.2.1</resource-property-value>
</resource-property-condition>
</resource-property-conditions>
<thresholds>
<threshold>
<name>lun:unaligned_reads</name>
<value>0</value>
</threshold>
<threshold>
<name>lun:unaligned_writes</name>
<value>0</value>
</threshold>
</thresholds>
<percentile>100</percentile>
<recommendation>Contact your support engineer.</recommendation>
</rule>