The build is done on our servers, we install the Android SDK, Crosswalk SDK, etc there. Updating the OpenSSL on your laptop is good to do, but should not affect how the APK is built. My guess is that google play is tweaking their scanning logic and the new apk gets rescanned and gets a different answer. It's a good idea to rebuild with Crosswalk 10, retest, and resubmit, even if you are not getting a warning right now.
I have no idea how the Intel XDK is working, but it maybe using files on your computer to assist in the build, so updating those helps. It maybe that when Intel XDK is updated this has the same effect as updating now with the links I have used.
It maybe none of the above and it might all be magic, but I suggest updating and trying to see if it works for you as it has resolved the issues for me. If this changes to being broken again in the future I will let you know.
Either way looks like it will be fixed if Intel are working on it too.
Oh and you dont need to use Cygwin I just installed that way which gave me the OpenSSL update. You can use the other link