Using BootIT, under the partition work menu there is the option to "slide" (it's off to the right) In the pop up menu that opens there is an option to "align for NTFS conversion."
I've never converted a boot partition (Well, the XP install....but I let it format the drive so, that doesn't count....), only extended partitions and seperate drives. I've encountered a few nagging errors, but after I've used BootIT to "align" they always go away.
I don't know how it works, it just does.
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