Elastic Beanstalk intermittently activates rack 1.5.2, but my Gemfile requires rack 1.6.0

I am running a standard Rails 4.2.0 app on Elastic Beanstalk. The container is the 64-bit Amazon Linux 2014.09 v1.0.9 box running Ruby 2.1.4, Puma 2.9.1 and Nginx 1.6.2.

When I push code to this environment, I get the following error in the puma.log: "You have already activated rack 1.5.2, but your Gemfile requires rack 1.6.0. Prepending bundle exec to your command may solve this."

I do not remember seeing these errors a few months ago when I was testing and it seems to be intermittent. Sometimes I push and everything works, other times I push and it fails.

http://ift.tt/19iUgtY suggests that there may be a bug in /opt/elasticbeanstalk/support/conf/puma.conf, but I've patched that file and the error still occurs. I've also made sure I have to have puma and rack in my Gemfile.

What is the most production ready and sustainable way to get my EC2 instances to load the right version of rack?