Breaking change for "Docker running on 64bit Amazon Linux 2" v3.6.2

After an automatic update of our Elastic Beanstalk environment (using Docker running on 64bit Amazon Linux 2) from 3.5.9 to 3.6.2 our server got completely broken. Has anyone experienced any similar issues? I haven't been able to diagnose the problem fully, but it clearly violates the rule of a minor update.

The server error I get is "FATAL: password authentication failed" when trying to connect to our database. The password is stored in a file called ".env-vars" (not .env for reasons irrelevant to this discussion). So maybe it's not properly reading the .env-vars file or affecting the database connection somehow?

If anyone can shed light on what is causing this issue, it would be greatly appreciated.