Found an explanation:
Kenneth G. Wilson (1923–). The Columbia Guide to Standard American English. 1993.
inalienable, unalienable (adjs.)
These two exact synonyms are still Standard, but inalienable, though a trifle younger than unalienable (both are seventeenth century words) is the more common today. Things inalienable [unalienable] cannot be given away, transferred, or otherwise removed.
It was the original draft in Jefferson’s handwriting that used “inalienable.”
http://www.ushistory.org/Declaration/unalienable.htm
As both words have the same meaning, I wonder why “un” was chosen over the original “in?” The “in” version rolls off the tongue easier, in my opinion, errr,, un my opinion!