After doing many researches, I found some remedy. Some are saying that this is a bug on chrome.
please refer too this link. https://stackoverflow.com/a/17972796/2276894
And also if you are targeting to create an admin/internal application, you can try Chrome App. It offers functions like, window.create()
with position parameters. You can control the position of the windows you created. Remember that you have to install the Chrome App you created in user's browser, just like in extensions.