Conflict between ruby & jruby bundle install

When I run the 'bundle install' command from the main directory of my ruby on rails (version 3) app, I get the following error:

Installing sqlite3 (1.3.3) with native extensions C:/jruby-1.6.0.RC2/lib/ruby/site_ruby/1.8/rubygems/installer.rb:529:in `build_extensions': ERROR: Failed to build gem native extension. (Gem::Installer::ExtensionBuildError)

In my path variable, I have ruby before jruby, so why is jruby being run? How can I resolve this issue? Thanks.

-Dan