I have Ubuntu Gnome 15.10 up to date and Chrome Version 48.0.2564.116 (64-bit). Gnome names my monitor as "secondary display" and TV as "primary display". TV is on the left hand side and monitor on the right.
When I open Chrome, it always opens in primary display. That is really annoying, as it is a TV and usually off or used as a TV. I always have to Super+Shift+Right arrow to get Chrome to my monitor.
The window that asks for password when I open Chrome opens in my monitor. I have several profiles in Chrome, they all open in secondary display.
How do I control where Chrome opens?