It's unclear whether you mean Freezing a window in the sense of it not refreshing or in the sense of locking the user out of going to the background window until they have done something in the front-most window.
A standard scripted Freeze window is only valid until a script step occurs which acts directly on a Window's display, such as a change in mode, or an explicit change in record or layout where some action takes place.
If you mean you want the front-most popup window to be locked in front until the user has interacted with it, not allowing them to click back into the background window, that requries some scripting, including setting Allow User Abort OFF.
If the script is paused on the popup window with user abort Off, and only a button on the popup can continue the script, then you can lock your user into the popup window.
In FMP12, we get a new Modal Window option which can be used to control this new feature without having to have a script paused. However, FM 11 and earlier require scripting with Allow User Abort OFF to accomplish the same thing.