Have you run http://zipdiff.sourceforge.net/ on this?
Yep, output shows 0 differences, and yet the two compared files have different sizes and, of course, one throws exceptions and one does not.
Tried with the new 2.5 release, same issue.
How does one turn this issue into an official Bug?
Sufficiently keep pressuring us to do so as you have done 
Can you expand on what your “Oracle application” is please. Just need some details on where the JAR doesn’t work for the issue title.
OK, will do. Willing to do a webinar, screencast, whatever is requested to get the team the data they need.
The Oracle product I am working with is called Oracle WebCenter Content.
The Oracle team also reports that they have a similar issue with other jars as well that are produced by open source and closed source projects. For example, I’ve heard they have a similar issue with a few of the jars produced by the Spring project. I’ve no idea if those jars are produced via Gradle, but I assume so…who doesn’t use Gradle anymore? 
Thanks, I’ve raised https://issues.gradle.org/browse/GRADLE-3320.
I’ve put this on our internal short list to look at. We’ll endeavour to look at it for the 2.6 release.