It has been my experience that the LabVIEW Application builder does an excellent job to retain the front panel automatically for any subVI that will ever need to show it while running.
I don't quite understand your syntax, because the application builder does not have an option to set "show front panel when run". A related VI setting is for example: "remove panel". It seems in your case, the panel gets removed. I suspect there is something unique in the way you interact with your subVI from the top level VI, fooling the application builder into thinking that the front panel is never needed. Does this particular subVI normally run in the background doing some computations and you later force passive visibility of the front panel with a VI reference? Is the VI "called by reference node" only? I would suggest to simply spent some time manually editing the build settings, then save the *.bld file for future use.
