Hi,
it seems that I have the same behavior. I've just installed KSP on Linux through Steam and noticed the exact same thing (freeze with mouse still moving). Running through strace I can see a syscall to futex() blocking. It *seems* that toggling “sync to vblank” to off fixes the issue for me. Unfortunately, it seems that this setting is never saved, I need to re-set it everytime. It might be related to the fact that KSP segfaults at exit, so maybe the settings aren't properly saved (although SYNC_VBL is set to False in settings.cfg).
Here are the information on my setup:
KSP 1.2.2.1622(LinuxPlayer) installed through Steam
Linux Debian (sid) x86_64 (doesn't matter if I run KSP.x86 through Steam or KSP.x86_64 through Steam or directly)
Intel graphics with i915 module and modesetting X11 driver
Xfce desktop environment (sync to vblank enabled in xfwm4 settings)
If you need something more, please ask.
In the end it looks to me like a vblank issue
it'd be nice to fix it but maybe there's not much which can be done in KSP (might depend on Unity3D or the graphics stack)
in any case, beeing able to save the setting and have it correctly applied would be nice