How to fix the inconsistent paragraph spaces in this MWE using KOMA?

Question

MWE code

\documentclass[twoside=semi, a4paper, 11pt, open=any, chapterprefix=false, toc=graduated]{scrbook} 
\usepackage{blindtext}
\usepackage{fontspec} 
\usepackage{libertine} %uncomment
\usepackage[libertine]{newtxmath} %uncomment 
\begin{document}
\chapter{Chapter One}
\blindtext[3]

\blindtext[1]
\section{Section One}
\blindtext[2]

\blindtext[3]
\chapter{Chapter Two}
\blindtext[4]

\blindtext[3]
\end{document}

Output -- unwanted spaces
enter image description here

Output -- desired effect

enter image description here

Question
How to fix this inconsistency in the same document? I noticed that by uncommenting the libertine lines of code the problem disappears.

Note
- compilation with XeLaTeX
This is XeTeX, Version 3.14159265-2.6-0.99991 (TeX Live 2014/W32TeX) (preloaded format=xelatex 2014.9.2)

This has nothing to to with KOMAscript or the libertine-package. The option twoside use \flushbottom as default, and the the spacing between paragraphs is stretched to flush the bottom of the pages. Add \raggedbottom to the preamble and the uneven spacing disappear. — Sveinung, Sep 18 '14 at 20:29
As Sveinung says. Basically a duplicate of Why does latex stretch small sections across the whole page vertically? I suppose? — Torbjørn T., Sep 18 '14 at 20:45

How to fix the inconsistent paragraph spaces in this MWE using KOMA?

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