This post is quite old, and from what I can see this is still an issue. I tried the mbralign tool from VSC 2.1.1 (most recent version as of this date) on a .vmdk on ESX 4.1 and it was unable to realign it. It did the scan the whole datastore thing.
I did download the 5.1 version and it worked like a charm (no corruption), but I still can perform scans using version 5.2.
I've not been able to locate a new, fixed version of mbralign. Does anyone know of one out there?