You can use the CompizConfig Settings Manager to control how windows are placed with multiple monitors. First you'll need to install it:
sudo apt-get install compizconfig-settings-manager
CCSM will now show up in the Dash or can be run from the command line with
In the "Window Management" category you should see a "Place Windows" button. Click on this and go to the "General" tab. You should see an option there called "Multi Output Mode" with a dropdown box. Try changing this to either "Use output device with pointer", which will open windows on the monitor where your mouse pointer is currently, or "Use output device of focussed window", which will open new windows on the monitor where the currently focussed window is located.