Sorry to necro this thread, but I'm seeing the same thing here.
I'd say our VMs are 97% Windows 2008 or 2012, 1% Win2k3, and 2% other.
On one LUN, I am seeing 75% misaligned reads & 50% misaligned writes. Another LUN (Citrix Xenapp servers on Win2k8) has 93% misaligned writes and all over the place with reads, between 10% and 80%. Another LUN is lower, around 20% misaligned reads & writes. The Exchange 2013 LUNs are beautiful with almost zero misaligned WAFL ops.
Netapp Balance reports 10 VM's out of alignment. We have 250+ VM's, so 10 is not a big percentage. However, in vSphere we don't have the option to align the VM's that Balance says aren't aligned.
Other info that might matter:
Our volumes were rebuilt after upgrading to ESXi 5.x to get them upgraded to VMFS5.
The LUNs on one controller of an HR pair seem to be less aligned than its partner. The controller with more misaligned traffic also has quite a bit more overall traffic in general.
We're using FAS 3270 with a bunch of 600GB 15k drives, some SATA 3TB + 4TB, and some 1.2TB 10k 2.5" drives. I believe we have two 1TB flash-cache modules. Data ONTAP 8.1.3.
VMware is all v5.1.