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I don't know anything about the internals of LabVIEW window management, so I can't speak to whether or not what you're seeing is intended behavior when the windows are reparented via winapi calls. Here's a VI that may help, though. This password-protected VI (saved in LabVIEW 2013) calls a private VI Server property to suppress LabVIEW editor dialogs. Call this VI before you do your scripting, with a TRUE input. Then when your scripting is done, call it again with a FALSE input to reenable LabVIEW editor dialogs. <standard disclaimer here about using private LabVIEW functionality in production code> Suppress Dialogs.vi