The confusion might come from thinking that libertarians are a homogenous group. To make a generalization: some groups of libertarians do value liberty as an end in itself, or the ultimate moral value; others see it as the logical extension of acting on a utilitarian calculus. Given my previous involved in the libertarian community and what I know about multi-system moral psychology, this seems plausible, if not obvious. [PDF warning]
But to an outsider researcher not already familiar with the libertarian movement/mindset, I can see how they wouldn't know that and how that lack of knowledge could skew the data into the contradiction you identified.
An article from the Wall Street Journal. The original title might be slightly mind-killing for some people, but I found it moderately interesting especially considering that many LessWrongers formed part of the data set for the study the article talks about and a large fraction of us identified as libertarian on the last survey.
Inside the Cold, Calculating Libertarian Mind
The original paper.
Understanding Libertarian Morality: The Psychological Roots of an Individualist Ideology