Consider scripting around the window's Glass Pane. Similar to Kyle's solution to the Modal Window problem....
.... but adding a glass pane to the specific Vision Window, not the whole client application. No clicks will get through to the components of that window. Unfortunately, this is not available at the container level.
Vision windows are type FPMIWindow, which inherit from JInternalFrame, which is why they can have a glass pane layer above everything else.