When clustering jobs by label, not all environmental variables are exported to the container.
In my tests I had one variable for the container and one variable for each of the two tasks in the labeled cluster.
What I observed was that the variable from the container and from the one of the two tasks was picked up, but the the environmental variable for the second task was ignored.
I was applying the env variables via profiles in the transformation catalog.

An example of a submit directory with this behavior can be found on workflow.isi.edu at:
/nfs/v5/georgpap/submit_folder.tar.gz