Originally Posted by OneMarcilV
Which version do you use?
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I just use whatever their latest free version is.
And actually I read up and looks like I was wrong- it doesn't fix misalignment automatically. But it does allow you to reformat and then copy the contents of your misaligned partition into the correct one during clone. Heres a link about it
Most likely this is a non issue for you though, because starting with Vista and above, windows formats its partitions correctly. But it still wouldn't hurt to check this after you do the clone. I would just get it cloned and worry about this later.