so I'm working with JMP 12 and I Made a GUI window that opens a JMP file.
but once the file is open, I can't click it unless I close the GUI window first.
for example I have this GUI, when I click run script it opens JMP table but every time I try to click, it doesn't open, unless I close the GUI

is there a way to be able to look at JMP files will the JMP GUI is open?
It sounds like your window has been opened as a Modal window. If that is the case, then it is working properly. A Modal window is designed to stop all processing until the window is closed.