OS type affects how LUN is created; "windows" assumes first partition starts at 63 sector so LUN layout is optimized for this. If you already created partition that matched this expectation, this won't change after you connect LUN to Windows 2008. If you created partition that did not match this expectation, you already had misalignment and this won't change after you connect LUN to Windows 2008.
Now if you completely wipe out LUN and create partition from the scratch under Windows 2008, then yes, you are likely to get misaligned partition because Windows 2008 by default starts partition at different offset.