Capt. Jack:
The most common cause for this phenomenon is that the "Floating Style" attribute is set to "Always" on your application's panel (in the UIR Editor, in panel properties under "Advanced"). Also, it's possible to run your panels as modal dialogs by using the InstallPopup() / RemovePopup() functions instead of DisplayPanel() / HidePanel(), which are more commonly used. Running a panel as a modal dialog can also cause this effect.
I hope this helps,
Chris Wood
Applications Engineer
National Instruments