I had a similar experience.
When i did a build and deploy on the a Start_up.vi i could see the front panel, but when I ran my application(Host) it did not open the front panel of my RT_applicaiton(RTEXE).
It appears that RTEXE type do not provide Front Panel as VI type . Even the Web Publish does not update.
You can alway "see" if your application is running via a Network Type Shared Variables linking your Host and RT application.