hi,
I guess you do have a while loop in your VI to allow for user input!!
It might be that the VI front panel is going behind the main panel. In which case you need to make the VI behave as a modal dialog. If you have TestStand 2 then there is an example ModalDialog in the examples folder. If you are still using Teststand 1.0.x then you can get the same example in the Resource Library. Do a search for Modal Dialog.
Hope this helps
Ray Farmer
Regards
Ray Farmer