Does not seem to be related to using a KVM switch. Had similar problems with directly connected KVM. The initial problem seems to be that the X configuration in firstboot writes /etc/X11/XF86Config whereas xorg reads the default /etc/X11/xorg.conf. Copying (or perhaps better moving - to avoid future confusion) /etc/X11/XF86Config to /etc/X11/xorg.conf will give the setup you supplied originally.
I can confirm that at least the monitor-type and graphics-card was written to /etc/X11/XF86Config. Most likely during firstboot.. But the HorizSync and VertRefresh lines in XF86Config are commented too.
Cheers, Hannes.