The test was to run the natively installed application from a empty ThinApp package. Utilizing the ThinApp runtime. Launching the old ThinApp package via this CMD is not going to help.
This test indicates that there is no serious issues running this application via our runtime. Which is good.
Next step I would do is to in your project folder (during dirty test, meaning the application is still locally installed) move the whole %SystemRoot% and %SystemSystem% folders into the Support folder and rebuild. This will keep those folders and there content from being included in the virtual environment. This way if the application starts we know there is something in those folders causing the issue. Since the application is locally installed will it find the dependencies locally so it should start.