It seems that the problem was that I had not commited .ebextensions
to git. Apparently, the file is read on initializing your application, so it has to be part of the bundle sent to elasticbeanstalk.
I had taken the idea of using the config file to set up the authentication keys from the amazon documentation http://docs.aws.amazon.com/elasticbeanstalk/latest/dg/create_deploy_nodejs_custom_container.html. However, I had not commited the file because it is clear that you are not supposed to commit your authentication keys (more on this discussion here: How do you pass custom environment variable on Amazon Elastic Beanstalk (AWS EBS)?).
I end up simplifying the file to contain the PARAM1 option, and I passed the secret key and access key id throughout the elasticbenastalk online interface.