Is your pop-up a subVI? If so, you can control it by using property nodes.
Inside the subVI place a property node on the diagram (from the app control palette). Right click and select Select Class>>VI server>>VI. This will allow you to control the properties for the VI. Then, select the property Front Panel Window>>Panel Bounds and wire the proper values into it. You can also do this from the calling VI, but that's more complicated.
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