So my question is why not simple: site.com/history

Same problem here with Joomla 1.7

Single article view 'history' becomes site.com/history/uncategorized/history
So does it mean site.com/title/category/alias ?

It should have an option to control this behaviour.
(Does the paid version have this option?)

Setting the 'Use Title or Alias?' doesn't make a difference in this behaviour. (alias and title are in my case the same..)