So it does return error code 0, thankfully. I've dropped the workaround on https://github.com/peterjc/galaxy_blast/issues/40 , and could do the pull request process in a few weeks.
d. ...
What is the error code? It might still be zero (which is fine for a warning only).
I've reopened https://github.com/peterjc/galaxy_blast/issues/40 for any potential Galaxy wrapper work around,
Peter