For a new Rails app running the Rails runner prefixed with jruby -S make Rails.root get the value uri:classloader:/. Starting without the jruby -S prefix works as expected.
$ rvm use jruby
Using /Users/uwe/.rvm/gems/jruby-9.0.0.0
$ gem install rails
Successfully installed rails-4.2.3
$ rails new test_app
create
...
$ cd test_app
$ ruby -S rails r "puts Rails.root"
uri:classloader:/
$ rails r "puts Rails.root"
/Users/uwe/workspace/jruby/test_app
The effect is the same with JRuby installed via RVM or by downloading and unpacking the JRuby 9.0.0.0 tarball.