My application GUI has a Component within its main window that uses an OpenGLRenderer. Whenever my TooltipWindow opens overlapping at all with that OpenGL Component, the overlapping portion of the TooltipWindow does not appear on screen. Is there any solution for this issue?
Not really - if you have an openGL component that doesn't fill the window, then it's implemented as an embedded window, so can't interleave with other lightweight components.
What you could do (and what I'd probably recommend in most cases) is to just use a GL context for your entire window, so that everything is rendered in GL as part of the same surface.