I have the same problem with Chromium 62.0.3202.94 running on Ubuntu 16.04. I want to launch two browser windows in app mode with each having a specific site and a specific location/position.
I'm using there options:
Second site: --app=
http://some.site --window-size=960,1000 --window-position=960,0
When I launch Chromium with these options, the second being launched always takes it's position from the first browser window and not from the --window-position parameter.
So, if I run the first, and then the second, I got two windows at 0,0. If I run the second, and then the first, I got two windows at 960,0. Really strange behavior.