Things started breaking for me with 'Factory not registered' errors. I tracked it down to adding the 'factory_girl_rails' gem to my Gemfile. Bundler autorequires it, which was causing FactoryGirl.definition_file_paths to already be resolved to spec/internal for it's factories.
I worked around it by disabling autorequiring in my Gemfile:
gem 'factory_girl_rails', :require => false
And then manually requiring it in my spec_helper.rb after Combustion.initialize!:
Combustion.initialize!
require 'rspec/rails'
require 'factory_girl_rails'
However, it might be nice if Combustion can somehow fix this.