My current setup for running a docker container is on the lines of this:
main.env
file:# Main export PRIVATE_IP=\\`echo
I had a very similar problem to this. If I passed the contents of the env file to docker as separate -e directives then everything ran fine however if I passed the file using --env-file the container failed to run properly.
Turns out there were some spurious line endings in the file (I had copied from windows and ran docker in Ubuntu). When I removed them the container ran the same with --env or --env-file.