Thanks for the reply
Ok, so it seems that even though the file itself did not change, the upgrader did apply the default permissions (644). This was unexpected, probably due to inexperience on our part. In other words, we expect that if a file had a material change (as detected by a merge utility for example, only then would the file be replaced/merged and file permissions reapplied.
It seems that when the file permissions are set to 644, this is the error that others with similar pipe configuration will see (error 127, meaning that the pipe.php file wasn't executable). Suggest adding to documentation if convenient, so that others can grasp an actual symptom resulting from incorrect pipe.php file permission.
Either way, thanks, and this can be closed.