If you only need to display a prompt and can get by with a limited set of canned buttons (OK, Cancel, Retry, Continue, etc.), you can try a VI that calls the Windows API MessageBox function. You can display a message box with user-defined title, text and buttons. There is an option to use the system modality which is what you want in this case. I use my own version of this all the time for that very reason.
Message Box