We are using rbenv to manage our gems and Bundler to manage our project with no customizations (i.e., no .bundle/config). RubyMine correctly detects the Bundler SDK's and if I add, for example, an rspec configuration, it works fine. However, it constantly complains about gems not being found, and in the "Ruby SDK and Gems" Setting I get the message "RubyGems not installed for SDK: rbenv: jruby-1.7.2". The SDK is installed in $HOME/.rbenv/version/jruby-1.7.2 and the Gems are in $HOME/.rbenv/versions/jruby-1.7.2/lib/ruby/gems/shared/gems.
If I try to execute, for example, a Rack configuration, it tells me that the rackup script is not found. Again, RSpec works fine.
Running RubyMine 5.4.1 on OS X Mountain Lion.