Have you changed the windows properties of the subVI to "dialog"? (VI properties..windows appearance).
... or if you "customize..." the apperance, make sure to select "Windows behavior: modal"
(Quote from the help:
Modal � Keeps the front panel on top of all other LabVIEW windows until you close the window or open another modal window. You cannot interact with other windows while a modal window is open. Most dialog boxes in LabVIEW are modal windows, such as the Options dialog box.)