I got this problem when deploying an application to a jruby environment with capistrano. The bundle:install task is done correctly but then it will report Bundler::GemNotFound if any gem in required in the next step.

With the help of Michal from rvm-capistrano, the problem is because the jruby on my server is installed in 1.8 mode as default and my application is running on 1.9 mode. After I reinstall it with rvm reinstall jruby-1.6.7 --1.9. Everything is correct again.

We think it could be a problem with jruby, just not sure if it still exists in 1.7.0

You could find all the information in here: rvm/rvm-capistrano#20