Remote app launches a "boarder less" RDP window of just the application without the normal RDP minimize/close/maximize button control. If you minimize the remote app, it goes to the thin client's taskbar and otherwise acts as if the application is running natively on the thin client.
That's what is happening. I just can't restore the window again afterward. The old way, with VMware View, we brought the whole desktop, but not anymore. I'm afraid I'm unclear about what you mean by the difference between a "real" remote app and a standard RDP shortcut. I can deploy the same app to Windows PC users via what I'd consider an "RDP shortcut" to the same server. However, on the thin client, I configure it with the server name/login info, and it shows the list of apps to choose from, then I tell it to automatically launch the right one. So, it's using the same mechanism/server as the shortcut PC users use, but the connection is 100% automated by the thin client (except for the problem I'm describing).
Based on chuckla's post, I found my way to a reg key for "RemoteDesktop_SuppressWhenMinimized" but that's client-side for Windows PCs. Not sure if the thin clients have an equivalent, or if that's what I need. Except for the thin clients, this is a Windows operation, so my "decoration" options (as I understand them) are limited - but that could point me back to GP changes I'm ignorant of. I don't know, and haven't found, how to serve up a maximized remote app with the min/max/x bar removed - which would be ideal.