Are you able to see any of the shader stuff at all if you remove some components or “leave holes” in them?
When I say “leave holes”: if you mark an OpenGLContext attached component as opaque but don’t draw into it fully, you will see the contents of the OpenGLRenderer in the “holes”. We use this in our plugins to create multiple “render views”, but it may be useful for debugging your app.
If it’s not even shown through those then something else may be wrong. If it is shown underneath components though… I’m not exactly sure where the problem lies then 
I know JUCE will disable depth testing when using the OpenGL-ified LowLevelGraphicsContext, but that shouldn’t be causing you issues AFAIK. They fiddle with the blending mode state as well in certain places…
What kind of graphics are you drawing over the component painting?