Unaligned VMFS partitions on the SAN decreases performance.

Creating VMFS partitions with Virtual Center 2.0 will align partition tables on the 64KB boundery and are not affected.
The expected throughput in a aligned partition increases by 2% to 62% and the latency decreases from 79% to 33%.
Partitions created with vmkfstools, created during the installation or migrated might be unaligned! For more information

Read the VMware Performance Study