On some computers KSP tends to open on the wrong monitor. This is more of a unity problem than a KSP problem and it took me quite a while to sort it out combing through forums.

It all resolves to the prefs file of Unity engine and the UnitySelectMonitor option in it. It usually contains the value -1 which probably means use whatever display is there.

My setup has a secondary monitor on the left side so setting this value to Zero fixed the problem.

<unity_prefs version_major="1" version_minor="1">
	<pref name="Screenmanager Is Fullscreen mode" type="int">1</pref>
	<pref name="Screenmanager Resolution Height" type="int">1200</pref>
	<pref name="Screenmanager Resolution Width" type="int">1920</pref>
	<pref name="UnityGraphicsQuality" type="int">5</pref>
	<pref name="UnitySelectMonitor" type="int">0</pref>
</unity_prefs>

Edit the file:

vi ~/.config/unity3d/Squad/Kerbal\ Space\ Program/prefs
 

Tested on Ubuntu 16.04 64bit and KSP 1.2.2.1622