Hi,
I've seen SQL LUNs in the past only doing partial writes (because of the nature of the DB which writes in 512B chunks) which could be misinterpreted as misalignment (or indeterminate). In this case wouldn't need to worry about it.
Windows 2008 LUNs shouldn't have issues with alignment (if you use the correct multiprotocol type as you have) as it uses a 1MB offset. You can check the offset in msinfo32 by going to Components-->Storage-->Disks, then checking the value of "Partition Starting Offset" - as long as it's divisible by 4KB then you should be ok.
Cheers,
John