SceneBuilder 1.1 is packaged with the packager.
If you open an Explorer then double click an FXML file A then SceneBuilder's launcher is called, the window comes up to front.
Then move back to front the Explorer window and double click a second FXML layout B: the issue (see DTL-5689) is that the second SceneBuilder window is rendered behind the Explorer one, only the blinking button in task bar alerts the user.

I suspect that the launcher code miss a call to AllowSetForegroundWindow.
I paste below an extract of the home written launcher of SceneBuilder 1.0, which isn't produced by the FX packager. See also RT-17836 for further details. At that time simply adding the call to AllowSetForegroundWindow solved the very same issue (could it be that simple ?).

    // Allow SceneBuilder window to open to the front (see RT-17836).
    // Possibly SceneBuilder should wait a little before it calls Stage.toFront()
    // to let time the foreground permission is granted to the FX process by Windows;
    // that said the tries I've made for now seem to show such sleep statement is not
    // necessary.
    AllowSetForegroundWindow(pi.dwProcessId);