After a day of tinkering around with this I realize this is an issue I am running into with Amazon Elastic Beanstalk. I tried to do everything to invalidate the Dockerfile (I'm not pulling the image from a docker repository to avoid the additional complexity, I am simply uploading to EBS from my jsreport folder). I tried creating a new environment under my existing EBS application, that didn't work.
The best solution seems to be to just start a new application up from scratch in EBS, which did work on the first try.
Thanks Jan