i was just facing this same problem with Rails4+minitest+zeus.
After i include gem "minitest-rails-shoulda"
in my Gemfile, zeus starts to run tests twice.
I just changed the gem orders at Gemfile and it solves!
Gemfile with Zeus running twice:
group :test do
gem "minitest-rails-shoulda"
gem 'minitest'
#...
end
Gemfile CORRECT:
group :test do
gem 'minitest'
gem "minitest-rails-shoulda"
#....
end