Missing Desktop Shortcuts with Native Engine ON

[sse123]

I have an installer that must run the native engine. This is because we have a step that requires we backup (zip) existing user files, run the installer, then unzip to restore user data. Based on reading the forums I believe this is a must, since the original installers did not mark the files as persistent/permanent. Turning on the Native Engine ensures the backup is created before the installer gets too far.

Unfortunately, on some machines the desktop shortcut does not get added. The desktop shortcut ALWAYS gets added when running without the Native Engine. The Desktop Shortcut does not always appear with the Native Engine Turned on. What could be causing this?

Here are a few things I have tried.

Making the Desktop Shortcut "Advertised" - didn't work.
Turning off Native Engine after the file gets zipped/unzipped. - didn't work.
Turning off Native Engine, after file gets zipped/unzipped, sleeping for a few seconds, then creating the icon again. - didn't work.

Your assistance would be most welcome.