If you don't mind an installer package rather than a Zip, this got around that 
problem for me.  It requires your Apple developer number (ABC...).  I run the 
app at least once from the Applications folder, and make no resource folder, 
etc... changes after that.  Then run this from the terminal.  

productbuild --component /Applications/MyApp.app /Applications MyApp.pkg --sign 
"Developer ID Installer: A Name (ABCDEFGHIJ)"

Some translation:
productbuild --component /WhereTheAppIsNow /InstallingPutsItHere 
installer.pkg.is <http://installer.pkg.is/>.created.here --sign "Developer ID 
Installer: KeychainName (ABCDEFGHIJ)"

See man productbuild in the Terminal.

Keith - CDI

> On Nov 14, 2016, at 9:45 AM, Robert Livingston <[email protected]> wrote:
> 
> Thanks for your input.
> 
> But I have tried using a DMG of the application and the same problem occurs.
> 
> 
> 
> 
>> On Nov 14, 2016, at 7:38 AM, spiffyguy <[email protected]> wrote:
>> 
>> Apple may change the permission from zip files as you experienced.  Perhaps
>> for mac it would be better to make a DMG of your app that people can
>> download from Amazon AWS.
>> 
>> They would get the "Are you sure you want to open..." alert when they opened
>> the DMG but your permissions would be fine inside the DMG.  Just have
>> instructions for them to copy it to the Applications folder or wherever you
>> would like them to run it.
> 
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