I observe this problem with both VcXsrv 1.19.2 and the Cygwin X server v.1.19.2. It affects GTK3 windows displayed from a remote machine running Ubuntu 17.04, but not Ubuntu 16.04. Ubuntu 17.04 uses GTK3 v.3.22.11 whereas 16.04 uses GTK3 v.3.18.9. This problem also affects Eclipse neon.3 when it is configured to use GTK3. The splash screen ends up offset, not in the middle of the screen. Then, the workspace selector window is so tiny that not even the corner "x" button to close the window is displayed...