multiple result windows for a Ruby script in Rails project directory

If I have opened Atom in a Rails directory with "atom ." to open the project, if I run a pure ruby script I get two output windows stacked on top of each other.

If I open Atom in a directory with just plain Ruby scripts in (again, with "atom .") and run the same script I get only the one output window as expected.

Not sure what is causing this? perhaps loading two environments when running (Ruby and Rails??)